Electrophysiology Python Packages

probeinterface

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

efel

Electrophys Feature Extraction Library

spikeinterface

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

elephant

Elephant is the Electrophysiology Analysis Toolkit

pyabf

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

mef3io

MEF 3.0 read/write - one C++ core with Python and MATLAB bindings. ~7-8× faster than the legacy pymef/mef_tools stack.

bluepyopt

Blue Brain Python Optimisation Library

mtscomp

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

phylib

Lightweight electrophysiological data analysis library

bluepyefe

BluePyEfe: Blue Brain Python E-feature extraction

kilosort

Fast spike sorting with drift correction

dartsort

A modular spike sorter written in Python and PyTorch

phy

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

bombcell

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

fenicsx-beat

Cardiac Electrophysiology solver in FEniCSx

jaxfne

Tensor-Field Neural Equations (TFNE) in JAX

ephys-mcp

MCP server for read-only analysis of intracortical (spike-level) brain-computer-interface recordings

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 Representational Similarity Analysis (RSA), & Inter-Subject Correlation (ISC)

cleosim

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

ephys-link

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

pieeg-server

One-line install for real-time biosignals: acquisition, processing, streaming, recording, visualization, and applications.

miv-os

Analysis pipeline for electrophysiology MiV-system and simulator

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.