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parameters.py
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parameters.py
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from brian2 import *
N_SST = 34
N_PV = 46
N_CC = 275
N_CS = 45
default = {
### General parameters
"duration": 10 * second, # Total simulation time
"sim_dt": 0.1 * ms, # Integrator/sampling step
"N_sst": N_SST, # Number of SST neurons (inhibitory)
"N_pv": N_PV, # Number of PV neurons (inhibitory)
"N_cc": N_CC, # Number of CC (PYR) neurons (excitatory)
"N_cs": N_CS, # Number of CS (PYR) neurons (excitatory)
### Neuron parameters
"tau_S": 16 * ms, # PYR neuron - soma membrane time constant
"tau_D": 7 * ms, # PYR neuron - dendritic membrane time constant
"tau_SST": 20 * ms, # SST neuron membrane time constant
"tau_PV": 10 * ms, # PV neuron membrane time constant
"tau_E": 1 * ms, # Excitatory synaptic time constant
"tau_I": 5 * ms, # Inhibitory synaptic time constant
"C_S": 370 * pF, # PYR neuron - soma membrane capacitance
"C_D": 170 * pF, # PYR neuron - dendritic membrane capacitance
"C_SST": 100 * pF, # SST neuron membrane capacitance
"C_PV": 100 * pF, # PV neuron membrane capacitance
"E_l": -70 * mV, # leak reversal potential
"E_e": 0 * mV, # Excitatory synaptic reversal potential
"E_i": -70 * mV, # Inhibitory synaptic reversal potential
"V_t": -50 * mV, # spiking threshold
"c_d": 2600 * pA, # back-propagates somatic spikes to the dendrites
"g_s": 1300 * pA, # propagates dendritic regenerative activity to soma
"g_d": 1200 * pA, # propagates dendritic regenerative activity to dendrites
### Sigmoid function params
"E_d": -38 * mV, # position control of threshold
"D_d": 6 * mV, # sharpness control of threshold
### Synpatic connection weights & probabilities
"wCS_CS": 0.27,
"pCS_CS": 0.16,
"wCS_SST": 0.05,
"pCS_SST": 0.23,
"wCS_PV": 1.01,
"pCS_PV": 0.18,
"wSST_CS": 0.19,
"pSST_CS": 0.52,
"pSST_CS_weight": 1, # represents fraction of `pSST_CS` for connection probabilities
"pSST_CS_soma": [0.5, 0.5, 1, 1], # represents fraction of `pSST_CS*pSST_CS_weight` going to the CS soma; {1-this} goes to CS dendrite
# `pSST_CS_soma` and `pSST_CC_soma` are taken in pairs
"pSST_CC_soma": [0.5, 1, 0.5, 1], # represents fraction of `pSST_CC*pSST_CC_weight` going to the CC soma; {1-this} goes to CC dendrite
"wSST_CC": 0.11,
"pSST_CC": 0.13,
"pSST_CC_weight": 1, # represents fraction of `pSST_CC` for connection probabilities
"wPV_CS": 0.32,
"pPV_CS": 0.43,
"wCC_CC": 0.24,
"pCC_CC": 0.06,
"wCC_SST": 0.09,
"pCC_SST": 0.26,
"wCC_PV": 0.48,
"pCC_PV": 0.22,
"wPV_CC": 0.52,
"pPV_CC": 0.38,
"wCC_CS": 0.19,
"pCC_CS": 0.09,
"wSST_PV": 0.18,
"pSST_PV": 0.29,
"wSST_SST": 0.19,
"pSST_SST": 0.1,
"wPV_PV": 0.47,
"pPV_PV": 0.5,
"wPV_SST": 0.44,
"pPV_SST": 0.14,
### Input amplitude & steady state
"I_sst_amp": 50,
"I_pv_amp": 50,
"I_cc_amp": 200,
"I_cs_amp": 100,
"I_sst_steady": 0,
"I_pv_steady": 0,
"I_cc_steady": 0,
"I_cs_steady": 0,
"lambda_cc": 10*Hz,
"lambda_cs": 10*Hz,
"lambda_sst": 10*Hz,
"lambda_pv": 10*Hz,
### Degrees for simulated orientation input
"degrees": [0, 90, 180, 270],
### Params for simulation analysis
"no_bins_firing_rates": 10, # Number of bins for firing rates historgram
"no_bins_isi": 16, # Number of bins for interspike intervals historgram
"plot_connectivity_graph": True, # If true, will also plot synapse connectivity graph for each simulation
"recompute_equilibrium": False, # If true, will try and recompute equilibirum time, if not will use `default_equilibrium_time`
"default_equilibrium_t": 0.2 * second # Default equilibirium time, will be used in case `recompute_equilibrium` is False. Should be set based on previous simulation results
}