simrun ❭ synaptic_strength_fitting ❭ PSPs
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 (
ParameterSet) – 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:¶
- 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
- 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:¶
- 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.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.Networkmapperfrom 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.