Electrophysiology Python Packages

efel

Electrophys Feature Extraction Library

probeinterface

Python package to handle probe layout, geometry and wiring to device.

spikeinterface

A Python-based module for creating flexible and robust spike sorting pipelines.

phylib

Lightweight electrophysiological data analysis library

mtscomp

Multichannel time series lossless compression in pure Python based on NumPy and zlib

elephant

Elephant is the Electrophysiology Analysis Toolkit

npyx

NeuroPyxels (npyx) is a python library built for electrophysiologists using Neuropixels electrodes. This package stems from the need of a pythonist who really did not want to transition to MATLAB to work with Neuropixels: it features a suite of core utility functions for loading, processing and plotting Neuropixels data.

bluepyopt

Blue Brain Python Optimisation Library

bluepyefe

BluePyEfe: Blue Brain Python E-feature extraction

kilosort

Fast spike sorting with drift correction

pyabf

pyABF is a Python package for reading electrophysiology data from Axon Binary Format (ABF) files

spikeextractors

Python-based module for extracting from, converting between, and interfacing with many common file formats in extracellular recording.

neurora

A Python Toolbox for Multimode Neural Data Representation Analysis - A Representational Analysis Toolbox for Neuroscience, including Neural Pattern Similarity (NPS), Representational Similarity Analysis (RSA), Spatiotemporal Pattern Similarity (STPS) & Inter-Subject Correlation (ISC)

bombcell

Automated quality control, curation and neuron classification of spike-sorted electrophysiology data. Available in MATLAB and in Python.

ephys-link

A Python Socket.IO server that allows any Socket.IO-compliant application to communicate with manipulators used in electrophysiology experiments.

hsmm-mvpy

Repository for the hmp python package

phy

phy: interactive visualization and manual spike sorting of large-scale ephys data

miv-os

Analysis pipeline for electrophysiology MiV-system and simulator

spectral-connectivity

Frequency domain estimation and functional and directed connectivity analysis tools for electrophysiological data

cleosim

Closed-Loop, Electrophysiology, and Optophysiology experiment simulation testbed for mesoscale neuroscience

spyglass-neuro

Neuroscience data analysis framework for reproducible research built by Loren Frank Lab at UCSF

emodel-generalisation

Generalisation of electrical models of neurons with MCMC

zpe-neuro

ZPE-Neuro V0.0: DETERMINISTIC NEURAL SIGNAL CODEC: Extracellular Spikes | Neuropixels | DANDI-Anchored | IBL Validated | Spike Train Transport

biopeaks

A graphical user interface for feature extraction from heart- and breathing biosignals.