Spike2 Spike sorting

Spike sorting

Spike2 classifies waveform shapes based on full wave templating on one or multiple channels both on-line and off-line. Spike2 includes single electrode input, stereotrode and tetrode capture and analysis. To complement the template matching, the software also includes clustering using Principal Component Analysis (PCA) and direct waveform feature measurements.

Main features

On-line and off-line spike sorting
Sort 8 spike types per channel on 32 channels on-line (more off-line)
Single electrode, stereotrode and tetrode recordings
Multiple sorting methods
On-line analysis functions
Synchronize multiple systems for recording larger numbers of channels
Display sorted spike classes from one channel as separate channels

Sorting methods
Template matching

Automatic or manual template generation
User-defined parameters for setting quality of fit
Compare, merge and delete templates
Templates can be fixed or can track changes to spike shape over time
Modify templates on-line
Saved templates can be loaded for use with different channels and files

Clustering
As an alternative to template matching, spikes can be sorted by cluster cutting. Values calculated by PCA or user-defined measurements are plotted to a 3D clustering window.

Cluster window

View can be rotated in 3 dimensions using mouse or sliders
K-means and normal mixtures algorithms for automatic cluster separation
Manual cluster separation by placing ellipses
View dots from a percentage of the entire time range and step through time to track moving clusters
Generate interval histograms based on displayed clusters
Show/hide particular clusters
Visual identification of clustered spikes occurring within a specified refractory period
Density plot option to aid cluster identification
Copy values as text (underlying data values and display co-ordinates)
Select individual spikes with a mouse click for manual classification

Principal Component Analysis

Select principal components to plot on X, Y and Z axes
Calculation of components for multiple trace (stereotrode or tetrode) channels based on entire waveform, peak amplitude or ratio of peak to mean amplitudes

User-defined measurements

Select measurements for X, Y and Z axes to cluster the data
Measure times, amplitudes, slopes and areas
Save up to 10 configurations containing different sets of measurements
For multiple trace data, measure individual trace or mean of trace measurements

Spike analysis functions
Built-in analysis functions for spike data include:

PSTHs
Cross correlations
Interval histograms
Rate displays
Mean and instantaneous frequencies
Spike-triggered averaging
Phase histograms

You can perform these analysis functions on-line and off-line, carry out further analysis with the script language or import the data into other software, for example Matlab.

Spike monitor
The resizable spike monitor window displays spike activity in a grid, with one grid cell per channel.

Display up to the last 40 spikes lying in a user-defined time range
Review spike activity from the current sampling time or at any time within the data file
Open the template editing dialog for a channel with a mouse click
Select display mode:
- 3D with spikes moving away through time
- 2D with all spikes overdrawn
- 2D with last spike shown separately from the overdrawn spikes
Show or hide duplicates of main spike channels

CED hardware
When used with CED 1401 interfaces, Spike2 enables you to capture continuous waveforms, event and marker data while sorting spikes in real-time and generating output stimuli.