biophysics_fitting¶
Generate and analyze biophysically detailed multi-compartmental models (MCM).
It provides two ways to generate mutli-compartmental models:
BluePyOpt [1], a Multi-Objective Evolutionary Algorithm (MOEA):
biophysics_fitting.optimizer
.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¶
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Check if a given section is connected to dendrites that reach beyon |
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Find all sections that are connected to dendrites that reach beyond a certain distance. |
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Given a Cell object and a section number, this method returns the branching depth (i.e. branching order) of that section. |
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Find the branching depth of the inner sections of a |
Find the main bifurcation of a cell. |
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Find all sections that are both inner sections, and are of branching order 1. |
Modules¶
Explore viable biophysical models from a given seedpoint. |
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Configuration and setup for simulating and evaluating biophysical models of Layer 5 Pyramidal Tract neurons according to the |
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This module provides method to set up the parameters for a Layer 5 Pyramidal Tract neuron (L5PT/L5tt) |
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This module provides the |
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The content of this module is mostly a reimplementation of the Hay et.al. 2011 methods used for extracting features. |
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Extract features from voltage traces. |
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Convenience methods to fetch biophysical models from a |
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Multi-objective optimization algorithm. |
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Fetch parameters with the dot naming convention. |
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This module provides methods to set up stimuli by adding recording/injection pipettes to |
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This module concerns itself with setting up a cell with biophysical details and simulation parameters. |
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Utility functions for biophysics fitting. |