Parameters

List of all the parameters used in the model

Parameter

Description

Default value

N_intrnrn

Number of interneurons

192

N_stell

Number of stellate cells

384

N_per_sheet

Number of cells in a ring (1D) or sheet(2D)

192

is_peak

Normalised synaptic strength of interneuron to stellate (I->S)

2

is_stdev

Width of I->S synapse

0.136

is_mean

Shift of the gaussian from the source for I->S synapse.
Symmetric on both sides of the source cell (neuron units).

32

si_peak

Normalised synaptic strength of stellate to interneurons

2.43

si_stdev

Width of S->I synapse

0.29

si_mean

Amount of offset from stellate to interneurons (neuron units)

22

ii_peak

Normalised synaptic strength of interneuron to interneuron

2

ii_stdev

Width of I->I synapse

0.136

ii_mean

Shift of the gaussian from the source for I->I synapse.
Symmetric on both sides of the source cell (neuron units).

32

N_per_axis

(For 2D) Number of cells along the length (or width) of each sheet

51

N_sheets_stell

(For Debugging) Number sheets of stellate cells

4

conn_id

ID for the configuration file for connectivity matrix

1d

instr_id

ID for the instrumentation config

1d

traj_id

(For 1D) Trajectory ID

vel_type

Type of velocity input to the network. (const, input, PRED-IHD, ACVT-1DAC)

const

input_id

(For single cell) Different types of pulse inputs used for single cell sims.

False

ss_syn_gmax

Peak S->S synaptic strength (\(\mu S\))

6.00E-06

si_syn_gmax

Peak S->I synaptic strength (\(\mu S\))

6.00E-06

ii_syn_gmax

Peak I->I synaptic strength (\(\mu S\))

0.0004

is_syn_gmax

Peak I->S synaptic strength (\(\mu S\))

0.0001

intrnrn_dc_amp

External DC input to interneurons nA

0.0015

stell_const_dc

External DC input to stellate nA. [right, left ] OR [east, west, north, south]

[0.0015, -0.00275]

stell_noise

Gaussian noise for stellate during simulation. [duration, mean, std]

[150, 0, 0]

stell_init_noise

Initial gaussian noise for stellate. [duration, mean, std]

[100, 0, 0.5]

intrnrn_noise

Gaussian noise for interneurons during simulation. [duration, mean, std]

[150, 0, 0]

intrnrn_init_noise

Initial gaussian noise for interneurons. [duration, mean, std]

[100, 0, 0.5]

noise_seed

Seed for simulation noise

0

init_noise_seed

Seed for initial noise

0

Amp_i_theta

Interneuron theta amplitude (\(S/cm^2\))

0.0001

phi_i_theta

Interneuron theta phase

0

omega_i_theta

Interneuron theta frequency (kHz).

0.01

stell_theta_Amp

Stellate theta amplitude (\(S/cm^2\))

0

stell_theta_omega

Stellate theta frequency (kHz).

0.01

g_h_bar

HCN maximal conductance (\(S/cm^2\))

0.0015

gnap_bar

Nap maximal conductance (\(S/cm^2\))

0.0005

hs_tau

Factor for HCN (\(\tau _s\))

5.6

hf_tau

Factor for HCN (\(\tau _f\))

0.51

n_phases

(Path integration) Number of cells between two grid fields

64

lambda0

(Path integration) Circumference of the circular enclosure

6.2831

init_allothetic_input

(Path integration) Turn on allothetic input

True

allothetic_stell_dc

(Path integration) DC to inactive stellate cells during allothetic input

-0.00265

allothetic_nrn_n

(Path integration) Number of neurons to pin for allothetic input

10

allothetic_dur

Duration of allothetic input

0

vel_integ_or

(Path integration) DC to inactive ring for path integration

-0.002906

si_asym_factor

Asym factor for S->I widths (Default values gives the original network)

[1, 1]

is_asym_factor

Asym factor for I->S widths (Default values gives the original network)

[1, 1]

is_peak_asym_fact

Asym factor for I->S peaks (Default values gives the original network)

1

is_mean_asym_factor

Asym factor for I->S mean(Default values gives the original network)

0

extra_params

Extra miscellaneous parameters

{}

netcon_delay

Delay for netcon spike transmission. (should >0 for parallel simulations)

1

sim_date_time

Date and time when the simulation was run

sim_dur

Duration of simulation

4500

dt

dt for NEURON integrator

0.025

sim_id

Simulation ID. Data files are named based on simulation ID.

0

sim_num

Simulation number for multiple simulations

0

split_sim

To split the sims into chunks for memory intensive simulation.
[state, duration_of_chunks]. Data is saved at the end every chunk. only for single simulations.

[False, 1000]

n_nodes

FF

1

n_cpus

Number of cores to utilize for simulations. If None then all available cores.

40

post_sim_analysis

Not applicable

False

show_progress_bar

Show progress bar for single simulation

False

recorder_dt

Time interval for recorders

1

data_root

Base location to save data. In case data needs
to saved at location different than the project root

data/

python

Not applicable

python

build_conn_matrix

To build connection matrix for every simulation. Alternative is to use a saved
matrix at network_configs/connections/saved_matrices/

True

save_conn_matrix

To save the built matrix

False

matrix_id

Matrix ID. Use to differentiate same matrix config built with different set of parameters.

split_built_conn_matrix

Not applicable

False

record_handle_stell

Recorder handle to record data from stellate cells.
{data_id: {“state”:False, “cells_to_record”:”all”, “loc”:”location of the reference variable”}

check default_sim_params.json for examples.

record_handle_intrnrn

Recorder handle to record data from interneurons.
{data_id: {“state”:False, “cells_to_record”:”all”, “loc”:”location of the reference variable”}|br|

check default_sim_params.json for examples.