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.

elephant

Elephant is the Electrophysiology Analysis Toolkit

bluepyopt

Blue Brain Python Optimisation Library

mtscomp

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

pyabf

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

phylib

Lightweight electrophysiological data analysis library

spikeextractors

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

kilosort

Fast spike sorting with drift correction

bluepyefe

BluePyEfe: Blue Brain Python E-feature extraction

jaxfne

JAX Tensor-Field Neural Equations (TFNE)

segovia

A fast, memory-bounded Rust engine for electrophysiology signal processing — Neuropixels-scale, callable from Python.

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)

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.

emodel-generalisation

Generalisation of electrical models of neurons with MCMC

ephys-link

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

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

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.

miv-os

Analysis pipeline for electrophysiology MiV-system and simulator

hsmm-mvpy

Repository for the hmp python package