![]() | Spike Train Analysis Toolkit |
We have developed an easy-to-generate input file format for the Spike Train Analysis Toolkit. Each input data set is described by two files:
.stad
file extension (example).stam
file extension (example – this example actually shows a .stap
file, in which the text "DATAFILE_FULL_PATH" is replaced with the absolute path of the date file, as described below, when the toolkit is compiled with make.m)This file format can hold information about spike trains ("episodic" data) as well as regularly-sampled data ("continuous" data).
The data file is a text file that consists of several lines, each line corresponding to a particular spike train or continuously valued parameter (e.g., LFP). Each line consists of a list of spike times or sampled values; each item in the list is separated by spaces. Each list can be associated with several recording sites and stimulus categories.
The metadata file is a text file that describes the data in the data file. The metadata file provides information about four types of elements (each described in more detail below):
datafile
site
category
trace
name=value;
There should be no whitespace on either side of the equals sign. The semicolon is required at the end of all statements. #
(the "hash" or "pound" sign) is taken to be a comment and is ignored.datafile
The datafile
consists of a name/value pair that gives the absolute path of the data file (i.e., not the path relative to working directory or the location of the metadata file).
datafile=/home/david/projects/cornell/data/rat/taste11.stad;
site
site
element consists of 5 name/value pairs: site
trace
elements to refer to the site. The first index is 1, not 0. This name/value pair must be given first.label
recording_tag
continuous
or episodic
.time_scale
time_scale=0.001
.time_resolution
time_scale
).si_unit
si_prefix
site=1; label=unit_001; recording_tag=episodic; time_scale=1; time_resolution=0.001; si_unit=none; si_prefix=1;
category
A category
element consists of 2 name/value pairs:
category
trace
elements to refer to the category. The first index is 1, not 0. This name/value pair must be given first.label
category=1; label=NaCl;
category=2; label=Quinine HCl;
category=3; label=HCl;
category=4; label=Sucrose;
trace
A trace
element consists of 6 name/value pairs:
trace
catid
trialid
siteid
catid
and trialid
, but differing siteid
s are assumed to be simultaneously recorded.)start_time
time_scale
to give the start time in seconds.end_time
time_scale
to give the end time in seconds. trace=1; catid=1; trialid=1; siteid=1; start_time=10.000; end_time=20.000;
trace=2; catid=1; trialid=2; siteid=1; start_time=10.000; end_time=20.000;
:
trace=16; catid=1; trialid=16; siteid=1; start_time=10.000; end_time=20.000;
trace=17; catid=2; trialid=1; siteid=1; start_time=10.000; end_time=20.000;
trace=18; catid=2; trialid=2; siteid=1; start_time=10.000; end_time=20.000;
:
trace=32; catid=2; trialid=16; siteid=1; start_time=10.000; end_time=20.000;
trace=33; catid=3; trialid=1; siteid=1; start_time=10.000; end_time=20.000;
trace=34; catid=3; trialid=2; siteid=1; start_time=10.000; end_time=20.000;
:
trace=48; catid=3; trialid=16; siteid=1; start_time=10.000; end_time=20.000;
trace=49; catid=4; trialid=1; siteid=1; start_time=10.000; end_time=20.000;
trace=50; catid=4; trialid=2; siteid=1; start_time=10.000; end_time=20.000;
:
trace=64; catid=4; trialid=16; siteid=1; start_time=10.000; end_time=20.000;