This section describes running loops with the pulseJacker. This feature is not required for mapping experiments; if mapping is a burning interest you can skip ahead to the mapping section if you like.
pulseJacker
For each relevant program (e.g. ephys, stimulator) the pulseJacker allows one to put out different pulses on different positions of a loop. For example, to generate an input-output function of a neuron (e.g. action potential frequency vs. current-injected) it is useful to sequentially inject a family of current steps and record the resulting membrane potential response.
Let's make a new pulse set ('ic' - for current clamp) and three pulses, injecting -50, 50, 100 pa currents (duration 100, delay 100).
Now bring up the pulseJacker program. Configure the pulses directory by selecting your pulses folder using Open on the File menu. To create a new pulseJacker cycle press New and save a file in the 'cycles' directory (here filename 'icSimple'). All changes to the pulseJacker settings are now automatically saved in this file.
Let's make three pulseJacker positions. Press 'Add' three times.
In pulse mappings select ephys: 700B-1-VCom. This is the only output we will configure. If you wanted to also use the stimulator you would have to repeat the procedure below for one or all of the stimulator channels.
Go to position 1 in the Positions panel. Pull up pulse set ic and select the -50pa pulse. On position 2 select 50pa, and on position 3 100pa.
Running a loop with pulseJacker enabled
Now run a loop with pulseJacker enabled: 'Enable' pulseJacker and put ephys on 'External'. Use the loopGUI to configure three acquisitions. The loopGui should be set to CPU timing mode, with an interval longer (by >0.5 sec) than the trace length in the ephys GUI (or stimulator, as appropriate). The iteration number should be set to the total number of sweeps desired. For example, to acquire all the sweeps for 3 positions in pulseJacker, this should be 3. To do them all twice, 6 iterations (and so forth). The position on the pulseJacker should also be 1, to start at the first pulse. To see all sweeps in the Acqusition window as they are acquired accumulate press the 'hold on' button in the toolbar (all the way on the right).
Note that the current trace is rendered as bright red, while the previous traces are darker. Right clicking on the acquisition window will make a bunch of other display options available.
Let's make a second hotswitch for the pulseJacker experiment.
Save configuration