_Setting up to acquire data
The set up procedures are very similar for in vivo electrophysiology, 2-photon, and intrinsic imaging experiments.
Identify your computing team: In each setup, there is a MASTER computer that coordinates all activity in the experiment and a STIMULUS computer that shows visual stimuli. In addition, there may be one or more additional specialized computers that perform other functions (such as a 2-PHOTON computer for controlling a 2-photon microscope or an INTRINSIC computer for collecting data from a CCD camera for intrinsic signal imaging, or other devices). It's important to identify each of these computers; in the VHLab, foghorn and leghorn (PCs) are the master computers for Rig 1 and Rig 2, respectively, and colonel and sanders (PowerMacs) are the stimulus computers for Rig 1 and Rig 2, respectively.
Turn on the MASTER computer and wait for it to boot up. Don't forget to wait before moving on to the next step.
Turn on the STIMULUS computer.
This computer should self-configure.
Verify on its "monitor" display (the second display, not the visual stimulus display) that Matlab opened and that the command line reports "Waiting for remote commands...PRESS COMMAND-PERIOD (APPLE-.) to interrupt".
If the computer does NOT self-configure, you can do it manually by 1) mounting the appropriate shared drive (so that your STIMULUS computer can see your MASTER computer), 2) running Matlab, and 3) typing initstims on the command line.
Turn on the visual stimulus monitor.
On the MASTER computer, run MATLAB.
On the command line, type RunExperiment.
Go to the "Data path" field and hit <return> to create a directory for today's date.
Click the Acquire data checkbox to turn on communication with any acquisition devices.
Open your acquisition environment.
Most experiments in the lab use the CED micro1401.
Turn on the CED micro1401.
On the MASTER computer, run Spike2.
In Spike2, from the file menu, choose "Load configuration". The configuration file we use is called "VHlab_config_leghorn.s2c".
Open the "script" file vhlab_spike2.s2s; typically, it will be one of the most recently opened documents and will be visible at the bottom of the File menu. Under the Script menu, go to the submenu Load and Run and then select the vhlab_spike2 from the list of opened scripts.
Many experiments in the lab use the Intan Technologies demo board.
Making sure to use the right power source (a 5V power source), plug in the Intan demo board. (Using the wrong power source will destroy the board.)
Plug in the USB connector from the MASTER computer to the Intan demo board.
Start the Intan acquisition program "RHD2000" on the MASTER computer.
In the RunExperiment figure window in MATLAB, click the appropriate button to open a new "sheet" for whatever experiment you are running.
If things go wrong while you are running a stimulus, you might want to check out Aborting a stimulus run.