Spike2 version 5 for Windows

Spike2 laboratory software delivers powerful data capture and analysis, stimulus sequencing and experimental control using one of the CED 1401 family of data acquisition peripherals. Specifically developed for life science research, Spike2 is already used in thousands of laboratories world-wide for a broad range of applications. Version 5 was once the latest release of this versatile software package; now see version 7.

Spike2 records a combination of waveform, event, digital marker, notepad, keyboard marker and sorted spikes. The total number of channels depends on your 1401 hardware configuration. Sampling can be continuous, timed or peri-triggered.

Waveform analysis includes averaging, power spectra, waveform discrimination and measurements such as area, gradients and RMS amplitudes. Analysis features are available both on-line and off-line.

Spike2 is easy to use. Its interactive interface provides all the data capture, data analysis and display control that most users require. Repetitive tasks, custom analyses and management of complex experiments can be automated with the built-in script language.

Spike2 features

Independent sampling rates for waveform channels to optimise data storage and analysis
Continuous, timed or peri-triggered capture of waveform and event marker data direct to disk
Text and digital markers for annotation and indication of external events and to facilitate selective review and analysis
On-line and off-line multi-channel analysis of waveform and event data with SD or SEM error bars and rasters
Automatic waveform feature detection and measurement
The ability to import a wide range of third-party data files
Automation and customisation of analyses and repetitive tasks
Digital filtering, curve fitting and data transfer between files
Trigger-hold display for oscilloscope-type view of responses
Measurements plotted into XY views or stored in data file channels both on-line and off-line
Signal processing options including rectify, smooth, re-sample, RMS amplitude and channel arithmetic
Powerful output sequencer to produce TTL pulses and analogue waveforms whilst sampling
Discrimination of single or multi-unit spike activity on multiple channels on-line and off-line
Single electrode, stereotrode and tetrode recording with spike sorting using templates and clustering by principal components or specified measurements. Clusters can be sorted automatically or by user defined ellipses

Data acquisition (requires a CED interface)

Record continuously or at timed or triggered intervals
Sample waveform inputs with different sampling rates on each channel
Log up to 8 channels of events to a very high resolution, typical sources include synchronising pulses or output from a waveform discriminator
Classify multi-unit spike activity into individual units on multiple channels
Generate and play out arbitrary waveforms for stimulus sequencing and control of experimental conditions
Play out pre-recorded arbitrary waveforms during data capture
Configure dynamically programmable amplifiers such as the CED 1902
Change quickly between experiment setups with a single mouse click
Automate file name generation and saving of a sequence of files
Calibrate waveform channels easily with result feedback to the sampling configuration
Access incoming data in real-time for very fast responses related to changes in waveform levels and detection of events
Synchronise multiple Power 1401 and Micro1401 mk 2 units to sample large numbers of channels with no time slippage between them

Experimental control and stimulus sequencing
Spike2 can handle complex experiment control and stimulus sequencing protocols during data capture by using the output sequencer. The sequencer controls up to 16 TTL and 8 analogue outputs with precise timing.

Sequencer outputs include square pulses, sine waves, ramps and pre-recorded or user-generated waveforms. On-line sequencer access to incoming waveform and event data enables very fast responses to changes.

The script language gives further experimental control options including communication through the serial lines and commands for starting and stopping other programs.

Spike sorting and clustering more details
Spike2 automatically creates templates from raw spike data based on user-defined parameters. All individual spike events crossing specified thresholds are captured and classified according to best match. Templates can be fixed or can track changes in individual spike shapes over time. You can also create templates based on clustering or by dragging a particular spike to a template.

On-line, up to 8 templates per channel can be used on up to 32 channels. You can monitor and modify the templates during data acquisition. Off-line, many more templates per channel are available.

Spike2 can cluster spike data using principal component analysis or user-defined spike waveform measurements. Clusters can be formed automatically or manually by cutting clusters manually using ellipses. 3D rotation of clusters and replay of activity enables better viewing of cluster formations. Interactive features include INTHs for current clusters, tracking clusters over time and selection of individual spikes by clicking on the cluster dialog.

Script language
Spike2 is a powerful package in its own right with the turnkey functions needed by most users. It can be further enhanced by the use of scripts.

CED script language features

High-level commands for performing complex analyses with a single instruction
Programmable toolbars, pop-up windows and dialog boxes for custom user interfaces
Familiar control structures (for...next loops, procedures, etc.)
Debugging tools including breakpoints, single-stepping and access to variable values
Script text editor with drop down function list, syntax colouring and split window options
Context sensitive help

Whilst many users write their own scripts, CED provides a script writing service and continues to develop and maintain a library of scripts. These are available to customers and provide a wide range of tailor-made functions including complex spike analysis and multiple stimulus control with associated analysis. Further customer and CED-written scripts are available to download.

To get you started writing scripts, the Spike2 package includes example scripts to use as templates, scripts that automatically generate code for toolbars and dialogs, a comprehensive script reference manual and a training manual with tutorials on a range of script writing topics. You can also write scripts by example! To do this, turn on script recording, do the actions to be recorded and turn off script recording. Spike2 will open a new window holding the script command equivalents of your actions.

Spike analysis On-line and off-line spike discrimination with cross-correlations, PSTH, INTH analysis and display of firing rates, detection and analysis of burst activity, spike triggered averaging and collision testing.

Action potentials Active cursors locate start times, peaks, troughs, maximum slope, re-polarisation percentage times, inflexion points, etc. on-line and off-line with automatic logging of measurements and values to text and XY views.

Evoked potentials Basic and conditional averaging with stimulus control, multi-channel EP component detection and measurement with waveform manipulation including smoothing, differentiation and filtering.

EMG Calculation and display of changes in EMG levels over time using either FFTs or area under curve, calculation of muscle fibre conduction velocity and plotting of EMG amplitude and force.

Cardiovascular Detection and measurement of waveform features e.g. QRS complex, Q-T intervals, systolic and diastolic values using active cursors, analysis of heart rate variability, R-R intervals, stroke cycle and Langdorff studies.

EEG On-line and off-line banded spectral analysis using scripts, automatic generation of results measured from built-in FFT processes to text and graphical format. Options include dominant frequency, power in frequency bands and cross-correlations.

Vision research Synchronised recording of eye position and neuronal activity with stimulus control, display of eye position, calculation of time on target and conditional analysis based on coded markers.

Sleep studies Simultaneous long term recording of multiple signals including EEG, ECG, EMG, respiration, temperature and sound sampled at independent rates; on-line and off-line analysis including Fourier analysis of EEG and EMG signals.

Behavioural studies Recording of animal activity with trial and stimulus markers, control of experimental conditions and reward delivery via RS232 and 1401 sequencer outputs.

Teaching Custom scripts run student practicals written to the exact specifications given by tutors. Requirements include the use of help files with experiment instructions and comparison of computer measured results with those of the student.

Version 5 features
Sampling

Sample many more channels with synchronised 1401s
Tetrode and stereotrode recording
Peri-triggered sampling with up to four channel groups
Multiple channel spike activity monitor window
Record multimedia video and sound, time-locked to Spike2 data
Improved data safety in the event of a system shutdown
Automatic measurement of waveform features

Analysis more details

Principal component analysis of spike shapes with 3D cluster display
Spike shape clustering based on amplitude, time area and slopes
Cursor dialogs extended to include cursor intervals as frequency, RMS error, mean and standard deviation of x range and measurements from events drawn as rate
Automatic plotting of markers and measurements into data file channels on-line and off-line
'Virtual' channels generated by user-defined expression. Can be used for waveform analysis, inter-channel arithmetic and converting event and marker data to waveforms
New text output option with re-sampling and interpolation for easy export to publishing packages
Interactive fitting of polynomials, exponentials, sinusoids, Gaussians and sigmoids to data in time, result and XY views

Control

Extended script dialogs have programmable buttons and can react to user changes while background script processes continue
TextMark drawing modes for displaying text in the time view. Markers have optional coloured "state" for condition marking
Cubic spline drawing mode in result views
Script control over spike templating dialogs

Future upgrades of Spike2 version 5 will be available to registered users free of charge as downloads from our web site.

Spike2 for Windows version 5 requires a CED Power1401, a Micro1401 or a 1401plus intelligent laboratory interface, and a PC with Windows 95, 98, Me, Windows NT 4, 2000 or XP. We recommend that the PC has a minimum of 256MB of RAM.