biophysics_fitting

Generate and analyze biophysically detailed multi-compartmental models (MCM).

It provides two ways to generate mutli-compartmental models:

  1. BluePyOpt [1], a Multi-Objective Evolutionary Algorithm (MOEA): biophysics_fitting.optimizer.

  2. An exploration algorithm: biophysics_fitting.exploration_from_seedpoint.

The MOEA does not require any a priori assumptions on biophysical parameters to find a MCM, but fails to explore the full diversity of possible MCMs. On the other hand, the exploration approach can explore the full diversity of possible biophysical models, but also requires a MCM as a seedpoint in order to start. If you need to generate models from scratch, we recommend using the MOEA algorithm to find at least a single model, and then using this as a seedpoint for the exploration algorithm.

Functions

connected_to_dend_beyond(cell, sec, beyond_dist, n_children_required)

Check if a given section is connected to dendrites that reach beyon beyond_dist.

get_inner_sec_dist_list(cell, select, connected_to_dend_beyond_distance, z_offset)

Find all sections that are connected to dendrites that reach beyond a certain distance.

get_branching_depth(cell, sec, beyond_dist)

Given a Cell object and a section number, this method returns the branching depth (i.e. branching order) of that section.

get_branching_depth_series(cell, z_offset)

Find the branching depth of the inner sections of a Cell.

get_main_bifurcation_section(cell)

Find the main bifurcation of a cell.

get_first_order_bifurcation_sections(cell)

Find all sections that are both inner sections, and are of branching order 1.

Modules

exploration_from_seedpoint

Explore viable biophysical models from a given seedpoint.

hay

Configuration and setup for simulating and evaluating biophysical models of Layer 5 Pyramidal Tract neurons according to the

L5tt_parameter_setup

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

combiner

This module provides the Combiner class and associated classes and functions.

ephys

The content of this module is mostly a reimplementation of the Hay et.al. 2011 methods used for extracting features.

evaluator

Extract features from voltage traces.

model_selection

Convenience methods to fetch biophysical models from a DataBase

optimizer

Multi-objective optimization algorithm.

parameters

Fetch parameters with the dot naming convention.

setup_stim

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

simulator

This module concerns itself with setting up a cell with biophysical details and simulation parameters.

utils

Utility functions for biophysics fitting.