stim file type

Stimfiles are IO files in Auryn with extension *.stim or *.stimtimes that contain a timeseries of stimulus activation time points. In Auryn a stimulus is characterized by the cells that are stimulated, i.e. a pattern of cells which is generally stored in a pat file.

Stimfiles are generated as an output of StimulusGroup which serves to keep track of the stimulation history, when this is generated randomly by StimulusGroup. However, they can also serve as an input to StimulusGroup.

The format of the file follows again a text standard which is directly interpretable by Gnuplot. It event based and features three columns. The first column denotes the time of the event, the second column contains either a 0 or a 1 depending on whether or not a stimulus is inactive or active. The third column contains the stimulus ID which has been loaded into the StimulusGroup and refers usually to a set (pattern) of cells.

A simple example of a stimfile could look as follows:

50.000000 0 0
50.000100 1 2
50.581800 1 2
50.581900 0 2
51.557600 0 2
51.557700 1 3
52.598500 1 3
52.598600 0 3
53.925900 0 3
53.926000 1 1
54.938600 1 1
54.938700 0 1

It is easiest to understand what is happening by looking at the gnuplot output of the following script

set border 3
set xtics nomirror
set ytics nomirror
unset key
set xlabel 'Time [s]'
set ylabel 'Active [0/1]'
plot 'test.stim' with lines lw 4 palette

which yields the following plot:

We can see that at t=50s stimulus 2 (brown) is activated and deactivated after about half a second. Shortly after that stimulus 3 (yellow) comes on etc …