Use ripple detection method of Kay 2016?

[edeno]

Our version of their code used their description of ripple detection in Karlsson, M.P., Frank, L.M., 2009. Awake replay of remote experiences in the hippocampus. Nature Neuroscience 12, 913–918. doi:10.1038/nn.2344:

SWRs were identified on the basis of peaks in the LFP recorded from one channel from each tetrode in the CA3 and CA1 cell layers. The raw LFP data were bandpass-filtered between 150–250 Hz, and the SWR envelope was determined using a Hilbert transform. The envelope was smoothed with a Gaussian (4-ms s.d.). We initially identified SWR events as sets of times when the smoothed envelope stayed above 3 s.d. of the mean for at least 15 ms on at least one tetrode. We defined the entire SWR as including times immediately before and after that threshold crossing event during which the envelope exceeded the mean. Overlapping SWRs were combined across tetrodes, so many events extended beyond the SWR seen on a single tetrode.

Which is what Jadhav 2016 uses as well. But a different detection method is presented in Kay, K., Sosa, M., Chung, J.E., Karlsson, M.P., Larkin, M.C., Frank, L.M., 2016. A hippocampal network for spatial coding during immobility and sleep. Nature 531, 185–190. doi:10.1038/nature17144:

Detection of SWRs was prerequisite for all data analysed in this study, and was performed only when at least three CA1 cell layer recordings were available. Offline, a multisite average approach was used to detect SWRs58. Specifically, LFPs from all available CA1 cell layer tetrodes were filtered between 150–250 Hz, then squared and summed across tetrodes. This sum was smoothed with a Gaussian kernel (σ = 4 ms) and the square root of the smoothed sum was analysed. SWRs were detected when the signal exceeded 2 s.d. of the recording epoch mean for at least 15 ms. SWR periods were then defined as the periods, containing the times of threshold crossing, in which the power trace exceeded the mean. SWR onset was defined as the start of a SWR period. Detection of SWRs was performed only when subjects’ head speed was <4 cm s−1. For SWR-triggered spike raster plots and PSTH plots, a 0.5 s exclusion period was imposed to isolate SWRs occurring only after non-SWR periods; otherwise, analyses of SWRs included all detected SWRs.

[edeno]

Loren Frank's lab seemed to think we should use the Kay method.

[edeno]

Also it seems that they've updated the method to smooth before combining tetrodes. I don't know if this makes much of a difference.

[edeno]

Current using. Closing for now