Granule and Basket Cells

This repository contains the Neuron and Arbor implementations and simulations of

1. A single basket cell
2. A single granule cell

Morphologies

1. The basket cell is a single soma model
2. The granule cell reads the morphology from output0_updated.swc in the morphologies directory

Density Mechanisms

The basket and granule cells both have the following mechanisms inserted on the soma and dendrites:

1. borgka.mod
2. cagk.mod
3. cat.mod
4. ccanl.mod
5. gskch.mod
6. ichan2.mod
7. lca.mod
8. nca.mod

There are 2 versions of the modfiles present in neuron/modfiles and neuron/modfiles_arb. The files in neuron/modfiles_arb have been edited to not use the TABLE feature which is supported in Neuron but not Arbor. Adding the TABLE feature is an optimization that changes the simulation results significantly. For accurate voltage measurement comparison, we use neuron/modfiles_arb for the neuron simulation.

For benchmarking performance, the TABLE feature (neuron/modfiles) can be used for the neuron simulations.

Parameters

Various parameters can be set in param_basket.json and param_granule.json.

Stimulus

A series of spikes is delivered to a synapse on the basket/granule cell. The spike times are read from param_basket.json and param_granule.json.

Running the examples

Neuron:

$ cd neuron
$ nrnivmodl modfiles_arb
$ python2 test_granulecell.py ../param_granule.json
OR
$ python2 test_basketcell.py ../param_basket.json

Running the examples will generate a plot

Arbor:

Installing Arbor:

• Install Arbor from the following branch: https://github.com/noraabiakar/usc_collab/tree/testing/new-revpot
• For help installing Arbor refer to: https://arbor.readthedocs.io/en/latest/install.html

Compiling the example:

$ cd arbor/granule
OR
$ cd arbor/basket

$ mkdir build && cd build
$ cmake .. -DCMAKE_INSTALL_PREFIX=/path/to/arbor/installation -DCMAKE_BUILD_TYPE=release
$ make

Running the example:

$ ./arbor-granule ../../../param_granule.json
OR
$ ./arbor-basket ../../../param_basket.json

Plotting the results:

Running the examples will generate voltages.json. To plot the results, you can use the provided tsplot script:

$ python2 tsplot.py arbor/granule/build/voltages.json
OR
$ python2 tsplot.py arbor/basket/build/voltages.json