glif_psc – Current-based generalized leaky integrate-and-fire (GLIF) models (from the Allen Institute)¶
Description¶
glif_psc
provides five generalized leaky integrate-and-fire
(GLIF) models [1] with alpha-function shaped synaptic currents.
Incoming spike events induce a postsynaptic change of current modeled
by an alpha function [2]. The alpha function is normalized such that an event
of weight 1.0 results in a peak current of 1 pA at \(t = \tau_\mathrm{syn}\).
By default, glif_psc
has a single synapse that is accessible through
receptor_port
1. An arbitrary number of synapses with different time constants
can be configured by setting the desired time constants as tau_syn
array.
The resulting synapses are addressed through receptor_port
1, 2, 3, ….
The five GLIF models are:
GLIF Model 1 - Traditional leaky integrate and fire (LIF)
GLIF Model 2 - Leaky integrate and fire with biologically defined reset rules (LIF_R)
GLIF Model 3 - Leaky integrate and fire with after-spike currents (LIF_ASC)
GLIF Model 4 - Leaky integrate and fire with biologically defined reset rules and after-spike currents (LIF_R_ASC)
GLIF Model 5 - Leaky integrate and fire with biologically defined reset rules, after-spike currents and a voltage dependent threshold (LIF_R_ASC_A)
GLIF model mechanism setting is based on three parameters
(spike_dependent_threshold
, after_spike_currents
, adapting_threshold
).
The settings of these three parameters for the five GLIF models are listed
below. Other combinations of these parameters will not be supported.
Model |
spike_dependent_threshold |
after_spike_currents |
adapting_threshold |
---|---|---|---|
GLIF1 |
False |
False |
False |
GLIF2 |
True |
False |
False |
GLIF3 |
False |
True |
False |
GLIF4 |
True |
True |
False |
GLIF5 |
True |
True |
True |
Typical parameter setting of different levels of GLIF models for different cells
can be found and downloaded in the Allen Cell Type Database. For example, the default parameter setting of
this glif_psc
neuron model was from the parameter values of GLIF Model 5 of Cell
490626718, which can be retrieved from the Allen Brain Atlas, with units being converted from SI units (i.e., V, S (1/Ohm),
F, s, A) to NEST used units (i.e., mV, nS (1/GOhm), pF, ms, pA) and values
being rounded to appropriate digits for simplification.
For models with spike dependent threshold (i.e., GLIF2, GLIF4 and GLIF5),
parameter setting of voltage_reset_fraction
and voltage_reset_add
may lead
to the situation that voltage is bigger than threshold after reset. In this case,
the neuron will continue to spike until the end of the simulation regardless the
stimulated inputs. We recommend the setting of the parameters of these three models
to follow the condition of
Note
If tau_m
is very close to tau_syn_ex
or tau_syn_in
, the model
will numerically behave as if tau_m
is equal to tau_syn_ex
or
tau_syn_in
, respectively, to avoid numerical instabilities.
For implementation details see the IAF Integration Singularity notebook.
Parameters¶
The following parameters can be set in the status dictionary.
Membrane parameters |
||
V_m |
double |
Membrane potential in mV (absolute value) |
V_th |
double |
Instantaneous threshold in mV |
g |
double |
Membrane conductance in nS |
E_L |
double |
Resting membrane potential in mV |
C_m |
double |
Capacitance of the membrane in pF |
t_ref |
double |
Duration of refractory time in ms |
V_reset |
double |
Reset potential of the membrane in mV (GLIF 1 or GLIF 3) |
Spike adaptation and firing intensity parameters |
||
th_spike_add |
double |
Threshold addition following spike in mV (delta_theta_s in Equation (6) in [1]) |
th_spike_decay |
double |
Spike-induced threshold time constant in 1/ms (bs in Equation (2) in [1]) |
voltage_reset_fraction |
double |
Voltage fraction coefficient following spike (fv in Equation (5) in [1]) |
voltage_reset_add |
double |
Voltage addition following spike in mV (-delta_V (sign flipped) in Equation (5) in [1]) |
asc_init |
double vector |
Initial values of after-spike currents in pA |
asc_decay |
double vector |
After-spike current time constants in 1/ms (kj in Equation (3) in [1]) |
asc_amps |
double vector |
After-spike current amplitudes in pA (deltaIj in Equation (7) in [1]) |
asc_r |
double vector |
Current fraction following spike coefficients for fj in Equation (7) in [1] |
th_voltage_index |
double |
Adaptation index of threshold - A ‘leak-conductance’ for the voltage-dependent component of the threshold in 1/ms (av in Equation (4) in [1]) |
th_voltage_decay |
double |
Voltage-induced threshold time constant - Inverse of which is the time constant of the voltage-dependent component of the threshold in 1/ms (bv in Equation (4) in [1]) |
tau_syn |
double vector |
Time constants of the synaptic alpha function in ms |
E_rev |
double vector |
Reversal potential in mV |
spike_dependent_threshold |
bool |
flag whether the neuron has biologically defined reset rules with a spike dependent threshold component |
after_spike_currents |
bool |
flag whether the neuron has after spike currents |
adapting_threshold |
bool |
flag whether the neuron has a voltage dependent threshold component |