synaptic_strength_fitting¶

Calculate the cell type specific synaptic strengths of synapses based on the neuron model and network parameters.

This module provides functionality to simulate each synapse in a network-embedded neuron model, calculate statistics per synapse type (e.g. mean, median and max voltage deflection). It can linearly interpolates the relationship between the synaptic strength and the EPSP statistics, and infers the optimal synaptic strength for each synapse type based on empirical data.

The main class PSPs is used to manage the synaptic strength fitting process.

Classes¶

`PSPs`	Calculate PSP amlitudes of single synapses and fit synaptic strength

Functions¶

`set_ex_synapse_weight`(syn, weight)	Set the synaptic strength of an excitatory `single_cell_parser.synapse.Synapse`.
`set_inh_synapse_weight`(syn, weight)	Set the synaptic strength of an inhibitory `single_cell_parser.synapse.Synapse`.
`run_ex_synapse`(cell_nw_generator, neuron_param, network_param, celltype, preSynCellID, gAMPA, gNMDA, gGABA, vardt, return_cell, synapseID, tEnd, tStim)	Simulate a single excitatory or inhibitory synapse
`run_ex_synapses`(neuron_param, network_param, celltype, gAMPA, gNMDA, gGABA, vardt, tStim, tEnd, mode)	Simulate all EPSPs of a given celltype, one by one.
`generate_ex_network_param_from_network_embedding`(confile)	Generate a network parameter file for excitatory synapses from a .con file.
`generate_inh_network_param_from_network_embedding`(confile)	Generate a network parameter file for inhibitory synapses from a .con file.
`get_voltage_and_timing`(vt, method, tStim, tEnd)	Calculate the maximum amplitude (and their timing) of an ePSP for all synapses.
`get_summary_statistics`(self, method, merge_celltype_kwargs, ePSP_summary_statistics_kwargs)	Calculate summary statistics of the EPSPs.
`get_optimal_g`(self, measured_data, method, threashold)	Calculate the optimal synaptic conductance such that the EPSP matches empirical data.
`get_tMax_vMax_baseline`(t_baseline, v_baseline, t, v, tStim, tEnd)	Calculate the ePSP amplitude.
`analyze_voltage_trace`(vTrace, tTrace)	Calculate a voltage trace’s extremum and time point thereof.
`get_tMax_vMax`(t, v, tStim, tEnd)	Calculate the maximum amplitude of an ePSP.
`merge_celltypes`(vt, detection_strings, celltype_must_be_in)	Concatenate the EPSPs of given celltypes.
`ePSP_summary_statistics`(vt, threashold, tPSPStart)	Calculate summary statistics of the PSP voltage and timing.
`linear_fit`(gAMPANMDA, epsp)	Calculate a linear fit between the synaptic conductance and the EPSP.
`linear_fit_pdf`(pdf)	Calculate linear fits between the synaptic conductance and the EPSP.
`calculate_optimal_g`(pdf)	Calculate the optimal synaptic conductance such that the EPSP statistics match empirical data.