Running an electrophysiology experiment

Lets start with your basicEphys configuration.

In this section we will use the stimulator and the acquirer. The hardware has been configured in your startEphus file (review startEphus). We will then define a particular set of program settings rapidly accessible using a hotswitch.

Acquirer

The acquirer simply acquires data from the configured Channels. We only have one channel configured ('photodiode'). If you want to use more channels (e.g. for a temperature probe, field recording etc) you need to configure these channels in the startup file (e.g. startEphus). Select the Acq On checkbox.

Stimulator

The stimulator puts out data. Our startup file configured a whole bunch of Channels corresponding to distinct hardware channels. It needs to be linked with the pulse directory (File\Open\ etc). Let's use 'shutter0' to drive a shutter. Make sure that all other channels have the Acq On checkbox deselected.

Make a shutter pulse (Width=100ms; Amp=5000 (note - this corresponds to 5 V); Delay=100) in a new Shutter pulse set and select it in the stimulator.

Running multiple programs simultaneously
Now select 'External' for the stimulator, acquirer, and ephys programs. All progrmas will now wait for an external trigger. Select Loop on the LoopGui to run three acquisitions.
The following should have happened:
The traces are displayed sequentially in the 2 acquisition windows
You should have heard the shutter opening (if applicable)
The traces are saved (as indicated by three new 'saved data' messages in the Matlab Command window)
02-Dec-2007 17:46:30 - Saved data to 'C:\Data\Gordon\cells\gs0001\gs0001AAAA0026.xsg'.
02-Dec-2007 17:46:33 - Saved data to 'C:\Data\Gordon\cells\gs0001\gs0001AAAA0027.xsg'.
02-Dec-2007 17:46:36 - Saved data to 'C:\Data\Gordon\cells\gs0001\gs0001AAAA0028.xsg'.
>>
In the XSG the acquisition number increments by three to ready itself for the next acquisition
 

Defining a hotswitch
Pull up the hotswitch and the hs_config programs. hs_config allows you to capature the configurations of individual programs to define a particular experiment. The hotswitch, once configured, allows you to rapidly get back to the relevant experimental settings. Defining a hotswitch is moderately cumbersome; but this is an extremely powerful feature that is at the core of Ephus functionality.

First, enter a hotswitch name (i.e., shutterCycle1) in the 'Name' block of the hs_config window. Then, via the 'Directory' panel, make a new folder in the hotswitches directory ('shutterCycle1') which will contain all of the relevant program configurations.
Now go through the program list and "capture" the settings for all of the programs that matter - not more or less. More might lead to slow response times; less would likely result in errors.

In this case we capture:

• ephys
• acquirer
• loopGui
• stimulator

There are different options for capturing states. The capture type (light and heavy) refers to the kind of configurations that are saved. The difference between light and heavy is largely program specific, however a light configuration generally does not contain GUI layout information. In this case, the different types of configurations have little or no bearing on the usage, and it is recommended to use heavy configurations.

There are two buttons used in capturing, 'Capture' and 'Capture All'. The latter will capture all active programs. In most cases this is unnecessary, and some users find that it leads to confusion. A typical best practice suggestion is to only capture those programs whose states you are interested in setting for the given hotswitch (i.e., ephys, acquirer, loopGui, stimulator; as above).

Now test the hotswitch. Turn off external triggering; the hotswitch should now recover external triggering on all three programs. Change the settings on the programs. The hotswitch should recover the previous state.

At this point it would be prudent to unselect all external triggering and save the configuration set.