Software

SpikeSorter

SpikeSorter is a Windows based program offering a complete set of tools for spike sorting from reading a raw data file to export of sorted unit times in csv and other formats. Supported input file formats include Plexon (.plx), Neuralynx (.ntt), Blackrock (.nev), Multi Channel Systems (.mcd), INTAN (.rhd) and, as of Version 5.0, Neuropixels spikeGLX and MCS HDF5 file types (plus limited support for other HDF5 types). Supported electrode types include single or multiple (up to 4000) channel MEAs, as well as single or multiple tetrodes and continuous or episodic recording. Processing functions include filtering, event detection, sorting, review and tools for merging and splitting clusters. Much of the code is multi-threaded. More documentation is included in help files that come with the program.

N.B. Windows 10 may give warnings when downloading. You may wish to scan the file to first make sure it is safe and then override the warnings about files that come from other computers

Version 5.0, released in February, 2022, includes a variety of improvements over version 4.71, including more extensive multi-threading, support for additional file types and much else.

Here is a file with simulated noise + spikes which can be used to demonstrate and test the various functions of SpikeSorter. There are 54 channels, with 60 units, each with 2000 spikes.


VRFX

Visual Receptive Field Explorer is a Windows program for demonstrating receptive field properties of neurons in the early visual system. It allows you to control and move a visual stimulus with the mouse over a simulated receptive field and listen to the spiking response on your computer audio. Receptive field types include retinal ON and OFF center neurons and cortical simple and complex cells.

N.B. Windows 10 may give warnings when downloading. You may wish to scan the file first to make sure it is safe and then override the possible warnings about files that come from other computers


Here are three Python packages used in the lab and developed by Martin Spacek:

  • dimstim – visual stimulus software
  • spyke – waveform data visualization and spike sorting software
  • neuropy – spike data and stimulus analysis software

Here is Keith Godfrey’s retinal waves simulation code.