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In Silico Framework

single_cell_parser

in_silico_framework

single_cell_parser¶

Cell API for single cell simulations.

This package provides functionality to parse Cell objects from NEURON .hoc files, map synapses onto these cells, and run biophysically detailed NEURON simulations with the resulting neuron-network models.

See also

This package should not be confused with singlecell_input_mapper.

This package is specialized to handle biophysical properties of neurons and simulation runs, and provides API access to the NEURON simulator [7]. It handles (among other things) synaptic activations onto a biophysically detailed neuron model.

singlecell_input_mapper provides extensive functionality to generate network realizations, constrained by empirical data. The results of such pipelines can be read in with this package.

Classes¶

`Event`	Class to handle events in NEURON simulations.

Functions¶

`create_cell`(parameters, scaleFunc, allPoints, setUpBiophysics, silent)	Creating NEURON cell models from cell parameters.
`init_neuron_run`(simparam, vardt, *events)	Default NEURON run with inital parameters according to parameter file.
`sec_distance_to_soma`(currentSec)	Compute the path length from :`sec(x=0)` to soma
`spines_update_synapse_distribution_file`(cell, synapse_distribution_file, new_synapse_distribution_file)	Update the .syn file to correctly point to spine heads as excitatory synapse locations.
`spines_update_network_paramfile`(new_synapse_distribution_file, network_paramfile, new_network_paramfile)	Update a Network parameters file to point to a new .syn file.

Modules¶

`analyze`	Analyze the results of single cell simulations and its network embeddings:
`cell_modify_functions`	Modify the cell after it is initalized.
`network_modify_functions`	Modify the cell and/or network after both have been initalized.
`network_param_modify_functions`	Modify the Network parameters.
`cell`	Cell objects for neuron models and cell activity.
`cell_parser`	Read and parse a `Cell` object from a NEURON .hoc file.
`network`	Connect and activate presynaptic neuron populations.
`network_realizations`	Create anatomical and functional network realizations.
`parameters`	Handle .param files in ISF.
`reader`	Read and parse .hoc, .syn, .con, and .am files.
`scalar_field`	Implementation of 3D scalar fields based on numpy arrays.
`serialize_cell`	Convert a `Cell` object to a serializable object and vice versa.
`sim_control`	Run a NEURON current injection simulation.
`synapse`	Synapse class for synaptic activations and NEURON API.
`synapse_mapper`	Basic synapse mapper to assign synapses to a neuron morphology, based on an existing synapse distribution.
`writer`	Write out anatomical, morphology or simulation data.