Note1: This page describes the RunExperiment environment. If you are looking for a checklist to help you run an experiment, it's best to look at Setting up to acquire data. Note 2: Alexander Heimel has made a separate and excellent manual, you can check it out here.
The RunExperiment environment is a set of GUI tools for controlling stimuli in the NewStim package and coordinating analysis for a wide variety of experimental data (including extracellular spikes, intracellular recordings, intrinsic imaging, and 2-photon imaging).
To get started (after all of the tools are downloaded and installed, of course):
- Run MATLAB, and then type RunExperiment. This will pull up the main RunExperiment window and the screentool window.
- The next step is to make sure the data path is set by setting the insertion point into the data path field and hitting <return>.
- If you wish to acquire data, make sure the acquisition list is set appropriately (that is, it describes the type of recordings you are about to acquire). In addition, click the [Acquire data] check box to make sure RunExperiment knows that you actually want to save the results of your data runs to disk.
- Next, open the experiment panel you wish to use for your recording / stimulation (such as ChR2Sheet, Multimouse, etc).
The idea behind RunExperiment is that you can create or use a stimulus and analysis control panel, called a sheet, that is tailored to your exact experiment, so that doing the experiment becomes much like filling in a form. The sheets help you organize your recordings, establish a common database, and make sure you've done everything similarly from experiment to experiment.
For example, one might open the channelrhodopsin experiment sheet by clicking [ChR2]. The ChR2Sheet then asks you if you want to look at record that you have already recorded (such as to review or reanalyze its data), or to look at a record that is yet-to-be-acquired. Click the appropriate box.
To use Spike2:
- Make sure the micro-1401 power is turned on, and start the Spike2 application.
- Open the appropriate script file that your lab uses (VHLab typical script is C:\Documents and Settings\vhlab\My Documents\vhtools\Spike2Scripts\vhlab_spike2.s2s). Note that when you select "Open" from the "File" menu you will need to make sure the "Files of Type..." selection is set to Spike2 scripts.
- Under the "Script" menu, choose submenu "Run script" and choose the script file you opened (such as vhlab_spike2).
- Now there is a tricky part; there are 2 start buttons, one at the top that has "[Abort]", "Trigger", and "Write", next to it (we'll call this the TOP Start button), and another one in the Toolbar that is for our script, with "[Wait for Start]", "[Stop]", "[SaveClose]" next to it), we'll call this the Toolbar Start. For this step, just notethe Toolbar Start and the button next to it (probably dimmed right now) that we'll call Toolbar [Stop].
- When you are ready to record, or when you are instructed to record by the RunExperiment package, for example, click the Toolbar [Start].
- At the conclusion of the recording, there is more trickiness; you have to click the correct "Stop" button, and there are 2 choices. click the Toolbar "[Stop]" next to Toolbar [Start] (not the Top Stop button).
- Click [SaveCloseRestart] to save and close, and re-run the script.
- You will be asked to complete spike waveform sorting; if you did not record any spikes using Spike2, then simply click OK. If you did, then proceed with this step.
- When you are all done, "[Start]" a recording with Toolbar start, and then click [Quit abort] to stop the script, and then you may exit Spike2.