❭ API reference ❭ biophysics_fitting ❭

hay

Example configuration for generating neuron models.

This module provides example configuration and setup for simulating and evaluating biophysical models of Layer 5 Pyramidal Tract (L5PT) neurons according to the methods described in Hay et al. [2], including:

  • Neuron model parameter setup

  • Target objectives

  • Simulation setup

  • Evaluation routines

While all of these components are usually defined by the user for use with either optimizer or exploration_from_seedpoint, and are specific depending on your specific experimental conditions, it can be of use to see how this example is configured as reference material. For example, the Simulator can be relatively abstract, to allow for a lot of flexibility. An example of how it is set up for L5PT neurons provides useful reference material to see what a Simulator object can and should do.

See also

get_Simulator() for an example setup of a Simulator object.

Modules

L5tt_parameter_setup

This module provides method to set up the parameters for a Layer 5 Pyramidal Tract neuron (L5PT/L5tt)

default_setup

A Python translation of the setup for in silico current injection experiments as described in Hay et al. [2].

evaluation

A Python translation of the evaluation functions used in Hay et al. [2].

setup_stim

This module provides methods to set up stimuli by adding recording/injection pipettes to Cell objects.

specification

This module provides convenience methods for Hay’s model specification (see Hay et al. [2]).

voltage_trace_visualizer

Visualize voltage traces from the results of a Simulator object.