burst & spike time analysis
This page contains downloadable scripts in the SPIKE2 script language, mostly written by Dirk Bucher. You need SPIKE2 version 4 or 5 to run them. Actually, version 4 may not work for some of the scripts. Most of the scripts are intended for the script bar. The script headers contain detailed descriptions.
You can download the short descriptions as a word file here. If you have questions, mail to Dirk.
!!! Instead of downloading script by script, here is a .zip file that contains all scripts (plus the word file). Don't worry, it's tiny (102KB) !!!
here's a link to wolfgang stein's scripts.
last update: 08/01/05
AddChan "Add up event channels"
As it says. Script to generate an event channel that holds spike times of two input event channels that you specify in the dialog.
batchImp "Batch import"
Allows you to convert all Axon files in one folder into Spike 2 files. VERY timesaving!
DelCur "Delete Cursors"
Deletes all cursors in a file (both vertical and horizontal).
displSwitch "display switch"
Script to switch the display in windows back and forth between spike2 default and a display with bold large font and x scale bar instead of x axis.
LineDraw "Set Draw Mode to "Lines"
Script to add to the script bar. Changes the draw mode of all event channels in a time view to "line" mode..
markerSwitch "enable/disable codes in marker channels"
Script to change fast which marker codes are on/off in a "0/1" markerchannel created with "mkburst" or 0/1 markers in a file converted from episodic stimulation in pClamp. For the script bar.'"markerSwitch".
NameChan "Name Channel"
Allows you to change the title of a channel.
Optimise "Optimise y-axis"
Optimizes the y-axis of all visible channels in the window. Same as "optimise all channels" in the y-axis menu. Just a shortcut for the script bar.
SubtrSpikes "Subtract events"
Allows you to substract events of one event channel from another one (with a timing tolerance to be specified). A new channel is created for the result.
TimeMax "Maximize x-axis"
Same as "view all" in the x-axis menu. Just a shortcut for the script bar.
WaveToEv "Waveform to Event"
Shortcut. Same as creating a buffer channel, importing a waveform channel, writing the buffer channel to a real event channel, and naming it. All in one go. Neat, isn't it?
WinDiscr "Window discriminator"
Allows you to extract events from a voltage window in a waveform channel.
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Burst and spike time analysis
burststat "Burst statistics"
Returns cycle by cycle burst parameters. Period, duration, duty cycle, spike frequency etc.
Counts the number of cycles of a fast (e.g., pyloric) rhythm per cycle of a slower rhythm (e.g., gastric). This includes the fractions of the fast cycles at the beginning and end of a slow cycle.
delFilter "delay filter"
sorts spikes according to different delay times between 2 recording sites.
gastropyloric"gastric pyloric interactions"
Script to do burst analysis of a fast rhythmic signal with respect to a slow rhythmic signal (as in pyloric/gastric).
IF_ISI "Instantaneous Frequency and Interspike Interval"
As it says.
missburst "missed bursts"
"Regularity check". Does burst statistics on a reference channel and counts the number of bursts in another channel for each reference cycle.
mkbursts "make bursts"
Detects burst starts and burst ends from spike times in an event channel and writes them to a marker channel.
phaseburst "Burst statistics & Phase Analysis"
Returns cycle by cycle burst parameters plus phase analysis for 2 or 3 neurons. Period, duration, duty cycle, delay, phase, etc.
Returns phase response values for reset/entrainment analysis. Can also look for changes in burst parameters.
pyloricPhase "pyloric rhythm phase analysis"
Customized version of "phaseburst". You don't have to assign anything in dialogs as long if you use the right channel names.
pylPhConsec "pyloric phase consecutive"
Script to do pyloric phase analysis (PD, LP, PY) from consecutive files. This is intended for large series of files but you can also use it for single files. It lets you do threshold based spike detection, burst detection and phase analysis all in one go. The idea is that it actually lets you look at every file so you can determine if your spike and burst detection went ok, but it keeps the spike detection thresholds and burst detection values between consecutive files.
rate_meanfreq "Rate and mean frequency"
Returns spike rates and mean frequencies per specified bin.
setBursts "create your own burst event channel"
script to create an event channel with bursts. You specify period, duration, #Spks, freq
WinSubtr "window subtraction"
Subtracts events from time windows set with mkbursts.
for batch processing:
These scripts work on a whole sequence of files, as long as the channel naming is consistent.
batch version of "burststat".
fast version for burststatistics. Returns only means and SD, not cycle by cycle values for every file.
batch version of "IF_ISI".
batch version of "rate_meanfreq".
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aab "area above baseline"
Measures area above baseline event by event.
InstCorr "Amplitude correlation"
Creates XY-plot from PSP amplitudes of two channels. Fast and ugly.
IVcurve "Current_ voltage relationship"
Returns data for IV plots. For square commands, measurements at 2 times.
MultiSweep "multiple sweeps"
As it says. Plots multiple sweeps of waveform data with fixed delay and duration from a trigger. Limited to 256 sweeps.
PSPparamAv "PSP parameters from average result files"
Returns parameters from averaged PSP. Cursor-based.
TrainPSPamp "PSP Amplitudes from train stimulations"
Returns EPSP/IPSP/EJP/EJC/EPSC/IPSC amplitudes in trains of events. Even when there's summation.
TrigPSP "PSP parameters"
Returns waveform analysis for triggered EPSPs/IPSPs/EJPs/EJCs/EPSCs/IPSCs.
Offset "Channel offset"
Allows you to add an offset to a waveform channel.
Plots difference between 2 multiple sweep XY views as created with "MultiSweep". For plotting difference current/voltage from episodic voltage or current clamp experiments.
XY_IVcurve "IV measurements from XY views"
Does IV measurements from multiple sweeo XY views, created from episodic clamp data with "multiSweeps"
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EMFsequ "Output sequence of metafiles from time windows"
Script to automatically output metafiles from sequential time windows of a time view.
TrigEMF "triggered metafile output"
Script to automatically output metafiles from time windows around a trigger event channel in a time view.
muscletransf "muscle force transfer function"
script to create muscle tension output from spike train event channel input using a te-at function. Based on Panulirus p1 muscle. See Chuck Geier's Thesis from Scott Hooper's lab.
isis_to_stim matlab script to generate complex stimulus files for pClamp from a list of interstimulus intervals
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