The analysis stage is initially for model validation and then subsequently for simulation-based investigations of brain function and dysfunction, diagnostic tools and possible treatments. The analysis step of Blue Brain’s workflow is supported by three open source software tools – the Electrophysiology Feature Extraction Library (eFEL), Blue Brain Python E-feature extraction (BluePyEfe) and NeuroM.
Blue Brain NeuroM is a Python toolkit for the analysis and processing of neuron morphologies.
Neuron morphologies are tightly coupled to neuron electrical properties and therefore are a crucial part of understanding the neuron as a functional unit.
The NeuroM software has been designed to enable researchers to quickly pinpoint the characteristics and specificities of every neuron. It is composed of a low-level API for reading morphology files on top of which are built several applications: a morphology file validator, a feature extractor and a morphology viewer. This software is also part of the Human Brain Project Brain Simulation Platform.
Blue Brain Python E-feature extraction (BluePyEfe) aims to ease the process of reading experimental recordings and extracting batches of electrical features from these recordings. To do so, it combines trace reading functions and features extraction functions from the eFel library.
BluePyEfe outputs protocols and features files in the format used by BluePyOpt for neuron electrical model building.
This software is also part of the Human Brain Project Brain Simulation Platform.
The Electrophys Feature Extraction Library (eFEL) allows neuroscientists to automatically extract features from time series data recorded from neurons (both in vitro and in silico).
Examples are the action potential width and amplitude in voltage traces recorded during whole-cell patch clamp experiments. The user of the library provides a set of traces and selects the features to be calculated. The library will then extract the requested features and return the values to the user. This software is also part of the Human Brain Project Brain Simulation Platform.