Python meets systems neuroscience: affordable, scalable and open-source electrophysiology in awake, behaving rodents


In-vivo electrophysiology, the recording of neurons in the brains of awake, behaving animals, is currently undergoing paradigm shifts. There is a push towards moving to open-source technologies that can:

  1. be adjusted to specific experiments;
  2. be shared with ease; and
  3. more affordably record from larger numbers of electrodes simultaneously.

Here we describe our construction of a system that satisfies these three desirable properties using the scientific Python stack and Linux. Using a Raspberry Pi to control experimental paradigms, we build a completely open-source, HDF5-based analysis (spike sorting) toolkit in Python.

This toolkit can be easily parallelized and scales to incorporate increasing electrode counts and longer recordings. Our rig costs about $5000, an order of magnitude less than many comparable commercially available electrophysiology systems.

Keywords:in-vivo electrophysiologyPythonopen-sourceHDF5spike sorting