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Spike2 Scripts


Analysis

Independent Component Analysis (ICA)
ICA15a.s2s & ICAutils.s2s (01/19)

icEEG.zip

ICA refers to a group of mathematical methods for separating sampled waveforms into statistically independent components. It is very useful for extracting the underlying signals from a group of recordings where each individual channel is an unknown mixture of signals from several underlying generators. For example, ICA offers a solution to the classical "Cocktail party problem": Can one disentangle individual voices from a conversational hubbub? ICA can do this provided that the sound was recorded from several different positions using multiple microphones.

ICA is also applicable in physiological recording situations where multiple electrodes are used to record underlying signals, for example, scalp EEG electrodes, intra-cranial multi-electrode EEG recordings, surface EMG recordings or electrode arrays in a tissue culture. Importantly, the method can also separate mains hum and sources of electrical interference from signals of physiological origin.

The price that you pay for excellent signal source separation is loss of amplitude information, - the results are normalised. However, if you can accept this limitation, ICA may be a very powerful form of analysis and well worth investigating.

The package includes:

ICA15a.s2s and ICAutils.s2s The main script and library of script functions
ICA15a guide.pdf User guide to the script
bssguide.pdf An introduction to the the maths underlying ICA
Sampled Sounds.smrx / .s2rx Example data containing a number of entangled musical tracks
icEEG example.smrx /s2rx Example data from 3 intra cranial EEG electrode arrays heavily polluted with mains hum

This script requires Spike2 version 9.

Rectify and Integrate waveforms
Integrate 01.s2s (06/16)

integrate01.zip

Extra-cellular multi-unit activity from peripheral nerves can be difficult to quantify. Individual units may not be identifiable because the signal to noise ratio is too low or too many units are activated simultaneously. In these circumstances, it can be helpful to rectify and integrate the signal over a short time range to convert the activity of an ensemble of units to a level that can indicate changing responses to stimuli. This script works on- or off-line on up to 4 source channels sampled at the same rate. You can increase the number of channels processed on-line by minor edits to the script.

This script has been tested with Spike2 v7.17 or higher.

Median value of a waveform
DoMedian01.s2s (12/18)

medianvw.zip

This script calculates 'median' value of a selected waveform between two cursors and tabulates results in the log view. The median is the mid-point of the data range, that is, half of the data points are lower and half are higher values. This measurement is not currently available from the Cursor Regions dialog.

Note that calculating the median could take a noticeable amount of time when the number of data points in the chosen range is large.

There is a user guide on page 1 of the script file.

The script requires Spike2 v7.20 or higher.

Grand Average
GrandAv 02a.s2s (12/18)

GrandAverage.zip

Use this script to build average views from multiple result views, i.e. PSTH's, interval histograms, waveform averages, and power spectra. Both source and destination views may contain multiple channels. There are manual and batch processing options:

  • Batch processing allows you to create a grand average from all of the result views in a folder. You can add each channel in the source files to the corresponding channel number in the grand average. Alternatively, you can add all channels in the source files to a nominated single channel in the grand average.
  • Manual mode: Here, you can choose which channel in the source to add to which channel in the destination grand average step by step.

Each channel in a multi-channel grand average view has its own sweep count held in the channel comment.

The user guide is on pages 1 -3 of the script file.

The script requires Spike2 v 7.11 or higher

Multiple cross-channel correlations
CrossChanCorrelation.s2s (09/07)

CrossChanCorrelation.zip

This script generates multiple spike correlation histograms for all combinations of templated spikes in a channel. Currently it allows for up to 8 spike templates per channel (including code 0) for correlating between channels in the file.

The script is controlled from a toolbar where the user can open a data file for analysis and control the parameters for the correlation as well as the number of correlation results views to display at any one time. A suitable example data file, Extracellular spikes.smr, is included in the Data folder of your Spike2 directory.

This script requires Spike2 v4.24 or higher.

Interactive feature detection
FeatureDetect.s2s (05/10)

FeatureDetect.zip

This script allows the user to interactively import peaks, troughs or threshold crossings based on an amplitude value defined with a pair of horizontal cursors, or a single horizontal cursor used as a threshold crossing.

The script utilises an idle routine that automatically updates the memory channel holding the event markers if the user adjusts the amplitudes or threshold levels. A suitable example data file, Blood pressure waveform.smr, is included in the Data folder of your Spike2 directory.

This script requires Spike2 v4.24 or higher.

Automate Cursor Regions Measurements
WMeasure.s2s (01/17)

WMeasure.zip

This script automates the process of taking multiple Cursor Regions type measurements. You simply specify the source channel, the type of measurement to take and the time range over which to make it. For example one could specify the mean of a waveform to be measured in 30s bins. The results can be plotted as a RealMark or tabulated in the log. As a further refinement you can specify a State channel and marker codes to gate the analysis to time ranges of interest.

This script requires Spike2 v6.06 or higher.

Fit a Gabor Function
GaborFitDemo.s2s (05/09)

GaborFitDemo.zip

The Gabor function is a sine wave damped by a Gaussian function.

This script allows you to fit a Gabor function to physiological data. An example application might be to detect oscillatory neural activity in auto-correlograms, e.g., Young et al (1992). The script also generates test data that you can use to familiarise yourself with the curve-fitting procedure.

You could also use this script as a template for fitting other functions by non-linear regression using the FitNLUser() script function.

This script requires Spike2 v6.06 or higher.

REFERENCE Young MP, Tanaka K, Yamane S (1992) On Oscillating Neuronal Responses in the Visual Cortex of the Monkey J NeuroPhysiol 67:1464 - 1474

Record and analyse respiratory data
Resp 80t.s2s (01/21) Improved!

RespRelease.zip

This archive contains scripts that enable you to:

  • Calibrate a pneumotachograph, the type of flow meter commonly used to record breathing
  • Convert the pneumotach. output to BTPS flow and BTPS volume online
  • Analyse respiratory data

The respiration analysis script enables you to:

  • Subtract drift from volume and flow traces
  • Measure inspired capacity (IC) and forced vital capacity (FVC) manoeuvres
  • Perform breath by breath analysis of many respiratory parameters
  • Plot Flow-Volume loops
  • Plot a composite maximal flow-volume loop using the script: Loop Env.s2s
  • Plot and tabulate slope ratio of Maximal Expired Flow-Volume loops
  • Investigate flow limitation during exercise by making comparative measurements of F-V loops
  • Plot Volume-Pressure loops
  • Measure elastic and resistive components of Work of Breathing

The archive also includes user guides, example data files and sampling configurations that should help you to get started. These scripts require Spike2 version 8.09 or higher.

They are beta versions. Send your bug reports and ideas for further development to geoff@ced.co.uk

LVP Analysis Resp Phases
LVP_Analysis_Resp Phases.s2s (06/21) New!

lvpanalysis.zip

In this Spike2 script, we use physiological left ventricle and tracheal pressure signals, obtained simultaneously by catheterization, to determine the interactions between cardiac hemodynamics and respiratory function. Metrics of systolic and diastolic function are calculated and separated into inspiratory, early expiratory, and late expiratory phases of respiration to characterize the effect of each respiratory phase on parameters of left ventricle function.

This script requires Spike2 v10.01 or higher.

On/Offline Measurement from a Blood Pressure Trace
HRBP8b.s2s (11/13)

hrbp_8.zip

This family of Spike2 v7 scripts and sampling configurations allows you to perform long-term recordings of blood pressure, heart rate and sympathetic activity and to analyse baroreceptor reflexes and heart rate variability. The scripts are suitable for use with a range of laboratory animals and can record data from up to 8 animals simultaneously when used together with telemetry systems.

HRBP8b.s2s derives systolic, diastolic and mean blood pressure, heart rate and respiratory rate from each blood pressure trace. Data from up to 8 animals can be analysed on- or off-line. Results are recorded continuously or according to a user-defined schedule, e.g. 10 minutes per hour. Data can be auto-saved to a new file at regular intervals (e.g. every 24 hr.) in order to achieve virtually continuous recording over days or weeks.

MergeFiles.s2s /SplitFiles.s2s These utility scripts allow you to splice auto-saved data files end to end before further analysis and to split data related to different animals into separate data files.

sBRG.s2s This offline script calculates baroreceptor reflex sensitivity based on spontaneous fluctuations in blood pressure.

SigFit.s2s Fits sigmoid curves (4 and 5 parameters) to heart rate and blood pressure data derived from steady-state experiments.

HRV1.s2s Performs frequency domain analysis of heart rate variability.

Poincaré s2s Performs non-linear analysis of heart rate variability.

HRBPtable.s2s Generates tables of results suitable for further analysis with spreadsheet software.

Baro5.s2s This is a library of script functions required by the SigFit script.

This family of Spike 2 scripts require v7.12 or higher.

Blood pressure analysis
HR_BP.s2s (05/21) Improved!

hr_bp.zip

This script allows you to:

Create additional channels in your data file derived from a blood pressure trace. The extra channels available are: Heart rate, inter-beat interval, diastolic bp, systolic bp, and pulse bp.

Process a single bp trace online or multiple bp traces offline.

Simulate online recording by replaying an existing time view using the REPLAY button.

Display a table of "current" blood pressure statistics that updates every second online or during REPLAY.

Generate a table of beat times and amplitudes for each derived channel in a grid view. This table can be saved or pasted into spreadsheet software for further analysis.

This script requires v8.20 or higher.

Amplitude histogram
amphist.s2s (06/07)

amphist.zip

This script generates an amplitude distribution histogram from a Waveform, RealWave or WaveMark channel. You can select the required channel, time range, amplitude range and bin size using a combination of cursor dragging and dialog entries. The results can be displayed in various forms including number of points, Time and percent time in each amplitude bin. A user guide is included in the comments at the head of the script.

This script requires Spike2 version 6,04 or higher. It also makes use of functions in the script file GHutils.s2s (included in the download). This file must be located in a folder called include located inside the directory holding your copy of Spike2.

Separate traces from stereotrode and tetrode channels
SeparateTracesNEW.s2s (09/13)

SeparateTraces.zip

This script will take a selected channel of multiple trace WaveMark data and create additional memory channels in the data file, each holding a single trace from the source channel. The user selectes the channel and type (stereotrode or tetrode) from a dialog when the script is run. A suitable example data file, Tetrode data.smr, is included in the .zip file.

This script requires Spike2 v5.21 or higher.

Detecting event bursts using Poisson Surprise
SURPRISE.S2S (05/98)

surprise.zip

This script detects bursts of events against a background of more random events.

Improved burst analysis
bursts.s2s (08/18)

bursts.zip

Create level channels in a data file that mark groups of Events, Markers or Wavemarks. Plot burst duration, inter-burst interval, burst period or events /burst vs time.

Create additional channels showing burst rate, burst onset times, and events within bursts and events not in bursts.

Generate a table of burst statistics that can be easily copied to a spreadsheet for further analysis.

Display a state channel marking low, intermediate and high levels of a waveform
Level indicator v1.02.s2s (09/10)

levelind.zip

For many applications it is important to know the timing and duration of periods when the level of a waveform channel exceeded a user-defined upper threshold, fell below a lower threshold or was between these levels. This script provides a convenient method of displaying and analyzing the number and duration of high, intermediate and low states.

The script allows you to do the following:

  • Set an upper and lower threshold level on the selected waveform channel
  • Create a level indicator channel in the data file with periods above, below and between the threshold levels denoted by coloured bars
  • Choose an appropriate colour code for the high, mid. and low states, e.g. red/amber/green or green/amber/red, depending on whether the high or the low level represents the 'optimal' or 'preferred' range
  • Plot the duration of an individual state or all 3 states as a function of time
  • Display the distribution of durations of each state as a bar chart
  • Generate a report suitable for further analysis with spreadsheet software
  • Use the normal data manipulation and analysis features of Spike2 during script operation

This script requires Spike2 version 5.09 or higher.

PSTH logging and integration
QPSTH2.S2S (12/98)

qpsth.zip

This script records trigger and response signals. It creates a PSTH result view and integrates it to produce a cumulative display. This is done on-line as the data is sampled. Two channels are defined: a trigger channel and a response event channel.

Histograms of instantaneous frequencies of events/markers in a time view
IF_distr01.s2s (02/18)

IF_distr.zip

This script creates a histogram of the distribution of instantaneous frequencies of events, Markers, RealMarks or WaveMarks in a Spike2 time view. It may be useful for plotting the frequency distributions of nerve impulse trains in response under various experimental conditions.

This script requires Spike2 version 8.03 or higher.

Automatic sleep staging for rats
Rat Sleep Auto.s2s (09/21) Improved!

RatSleepAuto.zip

This script assigns sleep scores (Wake, NREM, REM and Doubt) based on recordings from rate or mice of hippocampal EEG and nuchal EMG. It implements the method of Costa-Miserachs et al (2003). The script includes a user guide that should be read in conjunction with the original article: The zip file includes a data file that shows typical results and can be used to test the script.

Costa-Miserachs D, Portel-Cortez I, Torras-Garcia M, Morgado-Bernal I (2003) Automated sleep staging in rat with a standard spreadsheet. J.Neurosci Methods 130:93-101

This script requires Spike2 version 8.03 or higher.

On/Offline sleep-scoring for up to 4 animals
OSD4.s2s (07/21) Improved!

osd4.zip

This script is intended for on-line sleep staging in rats, mice or chicks. Sleep is divided into epochs of WAKE, NREM or REM sleep based on recordings of one EEG and one EMG channel per animal. The script can generate user-defined patterns of output pulses when a target sleep stage (e.g. REM) is detected. These pulses are suitable for controlling a laser in optogenetic studies.

The script is also suitable for simpler applications such as off-line sleep staging or plotting EEG spectral power in up to 4 frequency bands off-line.

Recording more than 2 animals simultaneously requires a breakout box (CED 2805 DIO-8) or a home-made custom cable in order to connect to digital inputs and outputs on the rear panel of a 1401 interface.

This script requires Spike2 version 8.08 or higher.

Manual sleep staging and event marking
sleepscore 705.s2s (09/17)

sleepscore.zip

This script allows you to perform the following tasks:

  • Subdivide a Spike2 time view into epochs of the desired length
  • Inspect the data and assign epochs to sleep stages (or other user-defined ategories)
  • Mark user-defined ‘Events’ such as apneas and arousals
  • Epochs and Events are shown as states in TextMark channels with different stages and events represented by a colour code
  • Mark Events and sleep stages under mouse control using a drag and drop method
  • Optionally display ‘skyline’ plots of EEG power in user-defined bands
  • Optionally display banded EEG power spectra of a selected epoch
  • Optionally display a hypnogram where each sleep state is represented by a level
  • Generate a report suitable for further analysis with spreadsheet software

This script requires Spike2 version 7.10 or higher.

Tabulate sleep-state -related changes in EEG spectral characteristics
PiB rept 06a.s2s (10/17)

PiBrept.zip

This script works on data files that contain one or more EEG channels and a sleep stage marker channel (a state channel with vigilance states marked by differently coloured bars).

You can create multiple EEG spectral channels, showing EEG power-in- band, dominant frequency or spectral edge. The script then generates a table of results showing the spectral characteristics of each successive episode of a user-defined sleep state (e.g. NREM) during a long term recording. This allows you to quantify changes in spectral characteristic with time and effects of optogenetic or other stimulation. The table generates a summary every hour or time interval of your choice so that trends can be identified more easily.

There is an option to “gate” the results, that is, to include or exclude data that falls in a time range around markers in a nominated channel.This means that you can, for example, exclude all data during stimulation, or include data for a specified time range after stimulation.

This script requires Spike2 v8.12 or higher.

Sleep staging using a machine learning algorithm
autoscore-1.85.s2s (03/22) Improved!

ssmla.zip

This script generates sleep scores for a rat or mouse based on one EEG channel and one channel of EMG from a neck muscle.

The script subdivides the data into short segments and allows you to score a subset of these epochs by visual inspection as WAKE, NREM, REM or UNCLEAR. These scores are marked in the data file in a colour-coded State channel. They serve as 'training data' for a machine learning algorithm that classifies the remaining epochs to best match the training criteria and returns the results in a second colour-coded state channel. The script has options to generate spectral power in bands, gated by sleep state and print results in spreadsheet format.

Requirements:

The script requires Spike2 v 10.04 or higher for full functionality.
In order to use the machine learning feature, a 64-bit version of Matlab with signal processing toolbox must be present and set up as an automation server.

The script has a detailed user guide that includes instructions on how to set up communication with Matlab. Further details on 'Troubleshooting the Matlab connection' are available via the Spike2 online help.

This script is based on software contributed by Henna-Kaisa Wigren and collaborators at the Institute of Biomedicine, Helsinki.

Import data from a Compumedics Profusion™ sleep scoring system
SS andEvts Import.s2s (04/16)

ssevtsimport.zip

This is a multi-stage process.

You can export the waveform data as European data format (.edf) and then import the .edf file into Spike2 for further analysis. However, data on sleep states and the onset and duration of manually scored events, -eye movements, apnoeas etc. are stored in a resource file (.xml format) that cannot be read directly by Spike 2.

Convert the .xml file to .txt format by copying the Profusion™ resource file from a web browser window to a simple text editor such as Notepad™ via the Clipboard and save it. You can then import the sleep stage and event information from the text file into the corresponding Spike2 data file using this script.

This script imports data saved in the CMPPSGSCOREDATA format.

There is a user guide in the comments at the start of the script file.

This script requires Spike2 v7.17 or higher.

Import data from a Compumedics Profusion™ sleep scoring system 2
SS -Evts Import 2.s2s (06/16)

ssevtsimport2.zip

This script works in a similar way to the previous script. However, it is intended to import text files created from .xml files in the Compumedics CMPSTUDYCONFIG format.

There is a user guide in the comments at the start of the script file.

This script is based on one contributed by Dwayne Mann, Biomedical Engineering, University of Queensland. If it works for you then it is thanks to him; if it doesn’t, you can blame me (GH).

This script requires Spike2 v7.10 or higher.

Import data from a Somnologica™ sleep scoring system
SS_imp_Somno.s2s (04/16)

ssimpsomno.zip

This is a multi-stage process.

You can export the waveform data as European data format (.edf) and then import the .edf file into Spike2 for further analysis. However, data on sleep stages are stored in a resource file (.xml format) that cannot be read directly by Spike 2.

Convert the .xml file to .txt format by copying the Somnologica™ resource file from a web browser window to a simple text editor such as Notepad™ via the Clipboard and save it. You can then import the sleep stage information from the text file into the corresponding .Spike2 data file using this script.

There is a user guide in the comments at the start of the script file.

This script has been tested with Spike2 v7,17 and 8.08.

Import sleep stages from a text file
Text-SS_Imp.s2s (06/19)

textssimp.zip

This script converts a list of sleep stages in a text file into a channel of colour coded sleep states in a time view.

It is intended to cope with the situation where waveform data but not sleep stages can be imported into Spike2 from a foreign data format. The text file to import may contain multiple columns of times, spectral powers etc. However, the script only reads 1 specified column that contains a list of sleep stage labels such as W, R, NREM etc.

You only need to specify the duration of a sleep stage and the start time of the first epoch. The script assumes that all epochs in the table are contiguous and of equal duration.

This script requires Spike2 version 7.17 or higher.

Sleep spindle / seizure detection
SleepSpindle 04.s2s (03/20) Improved!

sleepspindle.zip

Sleep spindles are brief bursts of 12-15Hz oscillations in the EEG during slow wave sleep. They occur in all the mammalian species that have been tested and are thought to be implicated in sensory processing and in the consolidation of long-term memories. Thus, there is significant research interest in the effect of learning, memory retrieval and pharmacological agents on the frequency of sleep spindles.

Sleep spindles are relatively small and somewhat variable and so detecting them automatically is not a trivial task.

This script attempts it by detecting bursts of EEG power in the relevant frequency band that exceed a user defined threshold. These bursts are then revised to exclude episodes that are shorter than a user defined duration (usually 0.5s) or to amalgamate bursts that are close together into a single event.

There are also options to exclude spindle-like events that exceed a set duration or exceed a threshold power level.

The results can also be gated to include only spindle--like events occurring within a specified sleep state.

The flexibility in setting these parameters mean that the script could also be useful for detecting other features such as seizures.

The script can process multiple EEG channels in a time view. The features detected are marked as coloured bars in State channels. You can also print the results to a spreadsheet or plot spindle count and spindle duration per epoch.

This script requires Spike2 version 8.16 or higher.

Mean and mean deviation
mean_angle.s2s (10/05)

mean_angle.zip

The purpose of the script is to calculate the mean and the mean deviation of a set of angles (or other variables) given by a textfile. In addition, it performs the Rayleigh test of uniformity, which tests whether the distribution of angles differs significantly from uniformity. The down-load contains the script and two test files.

Activity from Video
Activity from Video.s2s (03/20) New!

activity_video.zip

This script converts motion in a video recorded using the Spike2 multimedia facility into up to six "Activity" traces in the corresponding time view, logging movement in different user-defined areas of the frame. The script is intended for logging the activity of rats or mice or birds in adjacent cages videoed from above by a single webcam while other physiological signals (EEG, EMG etc.) are recorded. The activity traces can be used as part of the input to a semi-automated sleep staging process (e.g. OSD4.s2s, above).

The script does not attempt to track moving objects. It simply interprets changes in the grey-scale value of each pixel between frames as due to motion -rather than flickering lights, for example. This approach, though simplistic and qualitative, should provide an adequate indicator of movement in relatively homogenous environments.

The script works with avi and mp4 video files and requires Spike2 v10.02 for full functionality. It should work with some minor limitations in Spike2 version 9.10.

Some of these scripts have come from users rather than the CED team. If you have a script that you would like to offer to fellow users via this page, please tell Simon Gray. We provide some scripts for Signal too.

These scripts are stored as WinZip files, myscript.zip, except where they are shown as spike\scripts\myscript.s2s. Those latter files were installed with Spike2 and spike stands for the directory in which you installed Spike2. See the summaries by clicking on the description in the side menu. Then you can down-load them by clicking on the filename.

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Mains ‘hum’ is often complex and composed of odd harmonics of the mains frequency, making it very difficult to remove or suppress using simple high pass or notch filters. HumRemoveExpress.s2s is a Spike2 version 7 script that you can use offline to strip out much of this residual mains interference, making your data much more presentable and easier to analyse. This video tutorial shows how to use the script to remove mains hum.

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Registered in England: 00972132

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  • Technical Centre,
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Hardware: 84716070
Software: 85234945
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By email:

info@ced.co.uk

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  • Cambridge Electronic Design Limited,
  • Technical Centre,
  • 139 Cambridge Road,
  • Milton,
  • Cambridge CB24 6AZ
  • ENGLAND.
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