Realtime analysis of sweeps

[damianjwilliams]

Hi, I'm trying to plot the amplitudes of a series of sweeps in real-time. (I'm acquiring a sweep every 30 s, and would like to see how the amplitude changes over the course of the experiment). I believe that this can be done using the SweepFormula but I am getting lost in the documentation.

I can calculate the amplitude from the current trace and get the single value plotted in the SweepFormula plot, but I can't figure out how to get all the amplitudes from the previous sweeps plotted too.My code below. I'm not sure what comes next. I'd very much appreciate some guidance! Thanks

//define the regions of the trace where to take control and evoked measurements
t_range_control = [20,25]
t_range_evoked = [40,60]

//select the channel and all of the sweeps
sel = select(channels(AD0), sweeps())

//calculate the absolute values at control and evoked current 
dat_control  = min(data($t_range_control,$sel)
dat_evoked  = min(data($t_range_evoked,$sel)

//calculate the amplitude of the current
sweep_amplitude = $dat_evoked - $dat_control 

//plot the single amplitude value
$sweep_amplitude

[t-b]

I'm just guessing what the code is supposed to do but here is a version which plots something:

# define the regions of the trace where to take control and evoked measurements
t_range_control = [20,25]
t_range_evoked = [40,60]
sweepList = 1...10

# select the channel and all of the sweeps
sel = select(channels(AD0), $sweepList, all)

# calculate the absolute values at control and evoked current 
dat_control  = min(data($t_range_control,$sel))
dat_evoked  = min(data($t_range_evoked,$sel))

# calculate the amplitude of the current
sweep_amplitude = $dat_evoked - $dat_control 

# plot the single amplitude value
$sweep_amplitude

I changed the comment character to # from // and also tweaked the select statement. This now takes a list of sweeps using all visibility/mode. This means it does not look at the displayed sweeps which sweeps() returns with the implicit displayed.

You can get per operation help with selecting an operation name and hovering the mouse over it. When it should show you a tooltip.

For your application, plotting during data acquisition, I would enable Overlay Sweeps (OVS) and select the desired sweeps to plot. Then the sweeps() operation will pick up the selected sweeps and any new sweeps.

PS: We do have our SweepFormula documentation also available online at https://alleninstitute.github.io/MIES/user.html. But this is for MIES main which uses a different syntax for select and related operations.

PPS: You also might want to explore epoch information Settings->Visualize Epochs to not having to hardcode the extraction range but use a name like E1 for it.

[damianjwilliams]

Hi Thomas, Good guess as to what I was trying to accomplish! As I wanted to plot amplitudes from all the sweeps I just changed `sweepList = 1...10` to `sweepList = sweeps()` and it worked perfectly. Many thanks, Damian

[timjarsky]

@damianjwilliams Thank you for using MIES! May I ask how you ended up using it?

[damianjwilliams]

Hi Tim, I ended up using it as so: # define the regions of the trace where to take control and evoked measurements t_range_control = [20,25] t_range_evoked = [40,60] sweepList = sweeps() # select the channel and all of the sweeps sel = select(channels(AD0), $sweepList, all) # calculate the absolute values at control and evoked current dat_control = min(data($t_range_control,$sel)) dat_evoked = min(data($t_range_evoked,$sel)) # calculate the amplitude of the current sweep_amplitude = $dat_evoked - $dat_control # plot the single amplitude value $sweep_amplitude I'm using it as a way to monitor fEPSP amplitude over the course of an LTP experiment, in real time. I hope this answers your question! Thanks for your help. Damian

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