PSPs¶

class simrun.synaptic_strength_fitting.PSPs(neuron_param=None, confile=None, gExRange=[0.5, 1.0, 1.5, 2.0], AMPA_component=1, NMDA_component=1, vardt=True, mode='cells', exc_inh='exc', tStim=110, tEnd=150)¶

Calculate PSP amlitudes of single synapses and fit synaptic strength

Parameters:¶

neuron_param : NTParameterSet¶

The Cell parameters.

confile : str¶

Path to a .con file.

gExRange : list¶

List of synaptic strength values to simulate (in \(\mu S\)). The resulting ePSPs will be interpolated and compared to empirical data to find an optimal synaptic strength.

AMPA_component : float¶

NMDA_component : float¶

vardt : bool¶

Whether to use the variable step size solver.

mode : str¶

Whether to activate each synapse one by one, or each cell one by one. A presynaptic cell may have multiple synaptic connections with the neuron model (i.e. the Cell). Options: ('cells', 'synapses') Default: 'cells'

exc_inh : str¶

Whether to fit excitatory or inhibitory synapses. Used to infer the deflection direction of the PSP (positive or negative). Options: ('exc', 'inh') Default: 'exc'

tStim : float¶

Time of the synaptic activation. Should be large enough such that the membrane voltage has time to stabilize.

tEnd : float¶

End time of the simulation.

Attributes:¶

neuron_param¶

The Cell parameters.

Type:¶

NTParameterSet

confile¶

Path to a .con file.

Type:¶

str

gExRange¶

List of allowed synaptic strength values (in \(\mu S\)).

Type:¶

list

AMPA_component¶

Type:¶

float

NMDA_component¶

Type:¶

float

vardt¶

Whether to use the variable step size solver.

Type:¶

bool

mode¶

Whether to activate each synapse one by one, or each cell one by one. A presynaptic cell may have multiple synaptic connections with the neuron model (i.e. the Cell). Options: ('cells', 'synapses') Default: 'cells'

Type:¶

str

exc_inh¶

Whether to fit excitatory or inhibitory synapses. Used to infer the deflection direction of the PSP (positive or negative). Options: ('exc', 'inh') Default: 'exc'

Type:¶

str

tStim¶

Time of the synaptic activation. Should be large enough such that the membrane voltage has time to stabilize.

Type:¶

float

tEnd¶

End time of the simulation.

Type:¶

float

futures¶

List of futures returned by the dask client, containing the future results of the synaptic strength fitting simulations.

Type:¶

list

result¶

List of results returned by the dask client, containing the results of the synaptic strength fitting simulations.

Type:¶

list

network_param¶

The Network parameters for either excitatory or inhibitory synapses to be fitted. The synapse type is defined by exc_inh.

Type:¶

NTParameterSet

network_params_by_celltype¶

List of network parameters for each cell type in the network.

Type:¶

list

Methods:¶

_setup_computation(exc_inh)	Construct delayed functions for running single-synapse simulations.
run(client, rerun)	Run the single-cell simulations from the _delayeds.
get_voltage_traces()	Gather the ePSP voltage traces for each synapse.
get_voltage_and_timing(method, merged, merge_celltype_kwargs)	Calculate a PSP’s maximum voltage deflection and timing thereof.
get_summary_statistics(method, merge_celltype_kwargs, ePSP_summary_statistics_kwargs)	Calculate summary statistics of the PSP voltage and timing.
get_optimal_g(measured_data, method, merge_celltype_kwargs)	Calculate the optimal synaptic conductance such that the EPSP matches empirical data.
visualize_psps(g, method, merge_celltype_kwargs, fig)	Plot a histogram of the EPSP max voltage deflections for each celltype.
_get_cell_and_nw_map(network_param)	Get a network-embedded neuron model and its single_cell_parser.network.Networkmapper from parameter files.
get_synapse_coordinates(population, flatten, cell_indices)	Get the coordinates of all synapses of a particular celltype.
get_merged_synapse_coordinates(mergestring, flatten)	Get the coordinates of all synapses that contain a certain string in their name.
get_synapse_coordinates_with_psp_amplitude(population, g, merged, select_synapses_per_cell)	Get the synapse coordinates and the PSP amplitude for each synapse.
plot_vt(population, opacity, g, merge, merge_celltype_kwargs, fig)	Plot the voltage traces of the PSPs.