0. before you start
1. getting started
2. the @cortex class
3. creating a @cortex object
4. things you do with a @cortex object
5. the @key class
6. creating a @key object
7. the key file
8. working with @key objects
9. using @cortex and @key objects
10. spike data analysis
11. the @spix class

1. a quick "getting started" introduction

Suppose you have run an experiment in which a colorful stimulus was presented inside the receptive field of a visually responsive, isolated neuron. The experiment consisted of 4 different conditions, characterized by the color of the stimulus:

cnd #1: "red"
cnd #2: "green"
cnd #3: "blue"
cnd #4: "yellow"

At the end of the run, the data file collected by CORTEX contains a few hundred trials of randomly interleaved conditions. You now want to know the average response rate of the recorded neuron to the "blue" stimulus in a 200-ms time window starting 50 ms after the stimulus onset. Here's how to do that.

First you must create a @cortex object from the source data file, i.e., the file CORTEX created during the experiment:

>> c = cortex ('datafilename', 1:2);

The range [1:2] tells the function that this data file contains two trains of spike data encoded with the numbers 1 and 2.
Next, you create a @key object that will allow quick selection of an epoch and of trials that "belong together" in the experiment

>> k = key;
>> k.conds = 3;
>> k.start = 50;
>> k.finish = 250;
>> k.cue = 25;

the k @key object will isolate a time window starting and ending, respectively, 50 ms and 250 ms after the occurrence of event #25 in all trials of condition #3. You can now put things together:

>> mfr = meanfiringrate (c, 1, k)

which returns the average firing rate of spike #1 over said epoch for all trials that match the criteria specified by k.

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