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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.
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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'.
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In the XSG the acquisition number increments by three to ready itself for the next acquisition
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