RunExperiment environment

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):

  1. Run MATLAB, and then type RunExperiment. This will pull up the main RunExperiment window and the screentool window.

  2. 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>.

  3. 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.

  4. 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:

  1. Make sure the micro-1401 power is turned on, and start the Spike2 application.

  2. 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.

  3. Under the "Script" menu, choose submenu "Run script" and choose the script file you opened (such as vhlab_spike2).

  4. 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].

  5. When you are ready to record, or when you are instructed to record by the RunExperiment package, for example, click the Toolbar [Start].

  6. 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).

  7. Click [SaveCloseRestart] to save and close, and re-run the script.

  8. 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.

    1. Blah

    2. blah

    3. blah

  9. 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.