Software

Electrophysiology

• SpikeInterface: unified and open-source Python framework for spike sorting. Features include loading/saving in several file format, pre-, post-processing, running 10+ different spike sorters, validation (quality metrics - QC), export to Phy, automatic curation based on QC, comparison between sorting outputs, and visualization widgets.

• ProbeInterface: unified and open-source Python framework for handling neural probes.

• Open-Ephys plugins: collection of plugins for the Open-Ephys system
  • tracking-plugin: plugin for tracking animals and closed-loop stimulation based on real time position. It works in combination with Bonsai.
  • logic-gate-plugin: plugin to combine TTL inputs with logic gates.
  • sync-plugin: plugin to generate software-generated TTL that can be used to sync instrumentation.

• Pyopenephys: Python package to parse Open-Ephys recordings (openephys and binary format)

• Pyintan: Python package to parse Intan recordings (.rhd and .rhs)

• SpyICA: Python package for ICA-based spike sorting. Compatible with the SpikeInterface framework

• axon_velocity: Python package to reconstruct axonal branches from HD-MEA recordings

Simulators

• MEArec: Python-based simulator of extracellular spiking activity for spike sorting development and validation. Features include: replication of bursting, control of spatio-temporal collisions, slow and fast drifts, several noise models. Fully interfaced with SpikeInterface.

• MEAutility: Python package for defining and dealing with probe geometries and simulating electric potentials generated by electrical stimulation. It includes pretty plotting functions!

• nEuronMI: Python package based on FEniCS and Gmsh for simulating neuronal activity using the finite element method. It includes the full 3d-3d EMI model (Extracellular-Membrane-Intracellular) and it supports the hybrid solution.

Data management

• Expipe: Python package for lightweight managment of experimental projects. It includes a command-line interface (CLI) and it’s extendible with plugins to customize its use for different requirements.