A Visual Guide to Sorting Electrophysiological Recordings Using 'SpikeSorter'

Summary

The article shows how to use the program SpikeSorter to detect and sort spikes in extracellular recordings made with multi-electrode arrays.

Abstract

Few stand-alone software applications are available for sorting spikes from recordings made with multi-electrode arrays. Ideally, an application should be user friendly with a graphical user interface, able to read data files in a variety of formats, and provide users with a flexible set of tools giving them the ability to detect and sort extracellular voltage waveforms from different units with some degree of reliability. Previously published spike sorting methods are now available in a software program, SpikeSorter, intended to provide electrophysiologists with a complete set of tools for sorting, starting from raw recorded data file and ending with the export of sorted spikes times. Procedures are automated to the extent this is currently possible. The article explains and illustrates the use of the program. A representative data file is opened, extracellular traces are filtered, events are detected and then clustered. A number of problems that commonly occur during sorting are illustrated, including the artefactual over-splitting of units due to the tendency of some units to fire spikes in pairs where the second spike is significantly smaller than the first, and over-splitting caused by slow variation in spike height over time encountered in some units. The accuracy of SpikeSorter's performance has been tested with surrogate ground truth data and found to be comparable to that of other algorithms in current development.

Introduction

Anyone who records extracellular signals from the brain using methods more sophisticated than simple on-line thresholding and windowing faces the task of identifying and separating the signals from different neurons from the noisy voltage signals recorded by the electrode. This task is commonly known as spike sorting. The difficulty of spike sorting is compounded by various factors. Neurons can be very close together so that the signals recorded from them by a nearby electrode are likely to be similar and hard to distinguish. The signals produced by a single neuron may vary over time, perhaps because of movements of the electrode, variable sodium channel kinetics duri....

Protocol

1. Program Setup

1. Go to http://www.swindale.ecc.ubc.ca/SpikeSorter to download the program. Copy the supplied executable file to the directory of your choice. Read the accompanying documentation.
   NOTE: No formal installation or compilation is required.
2. Before opening any file to be sorted, ensure that there is enough free RAM to contain the entire duration of the recording. Also make sure a valid channel configuration file, as described in the documentation, is present in the same directory as the data file.
3. Start the program, then go to 'File - Open' and select the ....

Results

Figure 7 shows the display (obtained by going to 'View - Sorted waveforms') for a typical sorted recording. The default view option is just to show the waveforms on the center channel for each cluster. A common experience is that waveforms for a cluster pair on the same channel look identical, but when the 'Compare pairs' dialog is used to examine the two clusters there are distinct clusters in the PC projection, most often resulting from waveform differences on adjacent .......

Discussion

File Formats

Currently supported file formats include Neuralynx (.ntt and .ncs), Plexon (.plx), Neuroscope (.xml + .dat), MultiChannel Systems (.mcd), Blackrock (.nev) and Intan (.rhd). For unsupported formats, there are two options. One is to request addition of the file format to an upcoming release (an email link to the developer is provided in the 'Help - About' dialog). The other is to convert the file to a supported format. A simple option is to use the time-spike-format '.tsf&#.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
spikesorter.exe	N/A		http://www.swindale.ecc.ubc.ca/SpikeSorter