magic-maze

A MATLAB framework for running rat experiments through mazes using Arduino controllers.

The MagicMaze object

The core class is the MagicMaze object, which stores useful properties for running experiments.

• serial_port: contains the Serial object created when MATLAB connects to a serial port.
• protocol: a character vector that indicates which procedure to follow. This needs to be specified by the user. Outputs from the Arduino microcontroller are interpreted based on the protocol.
• exp_state: contains a human-readable explanation of what state MagicMaze thinks the current state of the experiment is. For example, it might be, "Rat running on treadmill".
• trials: a vector of doubles which contains values describing the trial type. 10 trials with two different conditions might be notated as a 10x1 vector of binary digits, for instance.
• outcomes: a vector of the same size as trials which contains the results of the experiment.
• isDone and isTreadmill: logical flags which give MagicMaze some flexibility in how to interpret output from the serial port.

Initialize a MagicMaze object

Simply bind the object to a variable. We will use mm.

mm = MagicMaze;

If MagicMaze is instantiated without a variable binding, it will create one (mm) and print a warning.

Upon initialization, the experimental state is set up 'startup'. For ease of experimenters during an ongoing project, the protocol is set by default to 'dmns'.

A timer object is also created. The MATLAB serial port callback API is woefully inadequate, so a timer is used instead to check conditions manually.

Setting experimental parameters

You can set the number of trials by assigning a vector to the correct property.

mm.trials = [0, 1, 1, 0, 1, 0];

Alternatively, to set n trials with values chosen from k, do:

mm.setTrials(k, n);
% example
mm.setTrials(1:4, 10);

To open up the serial port:

mm.setSerial;

If a port is not specified, MagicMaze will pick the first one. Otherwise, acquire the port by viewing the available ones using seriallist, and do:

mm.setSerial('port')

Performing an experiment

The doExperiment function is used to begin an experiment. It uses the specified protocol to determine what to do.

This means that each protocol needs to correspond exactly with the embedded Arduino-flavored C++ code on the microcontroller. For convenience, we have put this code in its own folder within this project.

As more protocols are developed, they can be added here.

PS: winny is cool