Spike Toolbox

Function index
Categorical

Spike train generation
Plotting functions
Spike train manipulation functions
Spike train analysis functions
Spike train stimulation and monitoring functions
Functions for manipulating addresses and addressing configurations
Address specification generation utility functions
Functions for managing toolbox options
General utility functions

Spike train generation
Spike train definitions
STCreate - Create a spike train definition
STCreateConstant - Create a constant frequency spike train definition
STCreateLinear - Create a linearly changing frequency spike train definition
STCreateSinusoid - Create a sinusoidally changing frequency spike train definition
STCreateGamma - Define a spike train using a gamma function for the ISI distribution

STInstantiate - Convert spike train definitions into concrete trains
STCreateFromVector - Package a vector of spike data as a spike train instance
STMap - Map a spike train to a specific neuron and synapse

Plotting functions
STPlotDef - Make a plot of a spike train definition
STPlotRaster - Make a raster plot of the spike train
STPlotInstFreq - Make an plot of the instantaneous freqeuncy of a spike train

2D Plotting functions
STPlot2DRaster - Make a raster plot of the spike train, differentiating between rows
STPlot2DISI - Make an ISI plot of the spike train, differentiating between rows
STPlot2DMeanFreq - ake a 2D plot of the mean frequency over a time interval of each pixel in a 2D array
STPlot2D - Make a 2D plot of the mean frequency over a time interval of each pixel in a 2D array

Advanced plots
STISIHist - Construct an ISI histogram for a spike train
STPSTimeHist - Construct a PSTH for a set of stimulus presentations

Spike train manipulation functions
STConcat - Concatenate spike trains in time

Manipulation of spike train mappings
STMultiplex - Multiplex spike trains in time
STExtract - Extract a single spike train from a multiplexed mapping
STFlatten - Convert a mapped spike train back to an instance

Manipulate a spike train in time
STCrop - Crop a spike train to a specified time extent
STNormalise - Shift a spike train to time zero and fix its duration
STShift - Offset a spike train in time

STSieve - Filter a spike train by Inter-spike interval

Manipulation of spike train levels
STStrip - Strip specified spike train levels from spike trains
STStripTo - Strip undesired spike train levels from spike trains

Spike train analysis functions
STCrossCorrelation - Calcualte cross-correlation for instantiated spike trains
STFindSynchronousPairs - Identify synchronous spikes in spike trains
STISIHist - Construct an ISI histogram for a spike train
STPSTimeHist - Construct a PSTH for a set of stimulus presentations

Spike train binning functions
STProfileCount - Bin spikes by a time window, and return the counts
STProfileCountAddresses - Bin mapped spikes by a time window, and return the counts for each address
STProfileFrequency - Calculate a frequency profile from a spike train
STProfileFrequencyAddresses - Calculate a frequency profile from a mapped spike train, for each address

Spike train stimulation and monitoring functions
PCI-AER stimulation and monitoring
STStimulate - Send a mapped spike train to the PCI-AER board
STPciaerImport - Import a spike train observed from the PCI-AER monitor
STPciaerExport - Export a mapped spike train to a file or to text

STStimServer - Send a mapped spike train to the spike server

Functions for manipulating addresses and addressing configurations
STAddrDescribe - Print information about an address

Logical and physical addresses
STAddrLogicalConstruct - Build a logical address from a neuron and synapse ID
STAddrLogicalExtract - Extract the neuron and synapse IDs from a logical address
STAddrPhysicalConstruct - Determine a synapse physical address
STAddrPhysicalExtract - Extract the neuron and synapse IDs from a physical address

Looking at address specifications
STIsValidAddrSpec - Test for a valid address specification structure
STAddrSpecDescribe - Pretty print an addressing specification
STAddrSpecCompare - Compare two or more addressing specifications

Validity tests
STIsValidAddress - Checks for a valid address for a given addressing specification
STIsValidAddrSpec - Test for a valid address specification structure
STIsValidChannelAddrSpec - Checks an address specification for use with channel IDs
STIsValidMonitorChannelsSpecification - Tests the validity of a monitor channels specification

Address specification generation utility functions
Utility functions to create addressing specifications
STAddrSpecIgnoreSynapseNeuron
STAddrSpecIgnoreNeuronSynapse
STAddrSpecSynapse2DNeuron
STAddrSpecChannel - Create a monitor channel address specification

STAddrSpecFill - Fill empty fields in a address specification

Validity tests
STIsValidAddrSpec - Test for a valid address specification structure
STIsValidChannelAddrSpec - Checks an address specification for use with channel IDs
STIsValidMonitorChannelsSpecification - Tests the validity of a monitor channels specification

Functions for managing toolbox options
Manipulating toolbox options structures
STOptions - Retrieve and set options for the Spike Toolbox
STOptionsLoad - Load Spike Toolbox options from disk
STOptionsSave - Save Spike Toolbox options to a file
STOptionsDescribe - Display info about an options structure

STToolboxDefaults - Creates a toolbox options structre containing the "factory default" options for the toolbox
STIsValidOptionsStruct - Tests for a valid Spike Toolbox options structure

General utility functions
STWelcome - Initialise toolbox and display welcome page

STDescribe - Print a description of a spike train toolbox variable
STTrainDescribe - Print a description of a spike train

Spike train level tests
STHasDefinition - Test whether a spike train has a definition
STHasInstance - Test whether a spike train has an instance
STHasMapping - Test whether a spike train has a mapping

Spike train tests
STIsValidSpikeTrain - Test for a valid spike train
STIsValidSpikeTrainLevel - Test for a valid spike train level description
STIsZeroDuration - Test for a zero duration spike train

STGetSpikeTimes - Extract spike times from a spike train

Spike Toolbox

Alphabetical function index