Sweep_response calculation and relationship with DF/F

[Leo454]

Hi all

I’m trying to pull out the neurons tuning curve to the drifting grating stimulus from Allensdk, and I get the heatmap but get confused about the DF/F %, maybe this is a very novice question. But I would be very grateful if anyone knows what does the % sign mean? I track the Allen’s code and find out the value calculated is from the sweep_response, I’m wondering how the sweep_response is calculated and is it related to the raw df/f trace?

Thanks

[saskiad]

I think I replied to this in part here:

What does the % in DF/F mean in the heatmap of tuning curve

DF/F is computed relative to a baseline. For the tuning curve for a stimulus, the DF/F is computed for each trial using the mean fluorescence during the 1 second prior to the trial as the baseline. This is computed as a percentage. See Figure 5 in the “Stimulus Set and Response Analysis” documentation here: http://help.brain-map.org/display/observatory/Documentation We also compute a “global” DF/F trace for each cell for the entire session which is accessible via the SDK. This uses a longer ba…

In brief, the sweep response is not computed from the df/f trace, but the DF/F is computed for each trial from the correct fluorescence trace.

Let me know if you have more questions about this.