Spike Train Toolkit
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  Spike Train Analysis Toolkit Input Structures

We have developed an easy-to-generate text-based input file format for use with the toolkit. Users can read properly formatted files with the provided staread function. This function returns a Matlab data structure that is compatible with the toolkit functions. Users have the option of bypassing the text-based file format by writing a script that puts their data directly into the Matlab data structure.

The Matlab data structure is described below:


  • Variable names are in gold.
  • Variable types are in green.

input (top level)

Holds information about the analysis input.

Name Description Type Size
M Number of stimulus classes in experiment int32 1
N Number of sites in experiment int32 1
categories Array of structures with categorized response data category M
sites Array of structures with recording site information site N


Holds information about the physical location(s) from which the data was obtained. In our framework, a data set should only contain multiple sites only if the sites were recorded simultaneously. Data from sites that were recorded sequentially should appear in separate input data structures.

Name Description Type Size
label Recording site label cell array 1
recording_tag Can be either continuous or episodic cell array 1
time_scale The scale factor required to convert the time mesurements in seconds double 1
time_resolution The temporal resolution of the recording (prior to scaling by time_scale) double 1
si_unit The pluralized international system of units (SI) base or derived unit of the sampled data char variable
si_prefix The international system of units (SI) prefix (a power of ten) double 1


The basis for the analysis is to determine how much information an ensemble of spike trains convey about some discrete stimulus attribute. The spike trains are partitioned into categories according to their stimulus attributes.

Name Description Type Size
label Stimulus class label cell array 1
P Number of response trials int32 1
trials Array of structures containing information about trials trial P×input.N


Holds information about single response trial.

Name Description Type Size
start_time Start time for the trial double 1
end_time End time for the trial double 1
Q Number of data points in the list int32 1
list An array with the data double Q


Weill Medical College of Cornell University