Computational protocol: Local or Not Local: Investigating the Nature of Striatal Theta Oscillations in Behaving Rats

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Protocol publication

[…] Data analysis was performed using custom-made Matlab programs (RRID:SCR_001622) and the FieldTrip toolbox (http://www.fieldtriptoolbox.org/, RRID:SCR_004849). First, the data were down-sampled to 1250 Hz. Faulty channels were discarded on visual inspection with NeuroScope (http://neurosuite.sourceforge.net, RRID:SCR_002455). Artifact rejection was completed using FieldTrip visual rejection function: for each epoch and channel, the LFP signal variance and z-value were computed over time and inspected to detect artifact. The remaining data were bandpass filtered from 0.1 to 250 Hz, and a notch filter was added to remove electrical noise artifacts (integer multiples of 50 Hz). We divided the continuous signal into two types of epochs. “Run” epochs included the last 5 s preceding the arrival of the rat in the stop area. During these 5 s, the rats were continuously running. The “baseline” epochs included 5 s of intertrial time before the start of the considered trial. [...] Spike sorting was performed semi-automatically using the clustering software KlustaKwik (http://klusta.readthedocs.io, RRID:SCR_014480) and the graphical spike sorting applications Klusters (http://neurosuite.sourceforge.net, RRID:SCR_008020) or KlustaViewa (http://klusta.readthedocs.io). Spike-LFP coupling was examined by producing phase histograms using FieldTrip function ft_spiketriggeredspectrum. Units yielding <20 spikes in total (across all the considered epochs) were excluded from the analysis. All units were visually inspected and, if several clusters corresponded to the same cell, supernumerary clusters were removed. To calculate the significance of spike-LFP entrainment, two metrics were computed: the Rayleigh p value (testing the nonuniformity of the circular distribution) and the pairwise phase consistency (PPC) values (). We found good accordance between these two methods in most cases, although on some instances (for low-frequency modulated cells; see Results) the Rayleigh p value was not specific enough of the frequency of entrainment. Hence, we considered cells as being specifically entrained to the theta rhythm if they also presented a maximum PPC at 8 Hz. To quantify the strength of the entrainment and the preferred phase for each unit, we hypothesized that the spike-phase distribution followed a von Mises distribution and we computed the concentration factor kappa κ and the preferred phase θ () using the Matlab Circular Statistics Toolbox (). We worked on the following data set for the analysis of spike-LFP entrainment: […]

Pipeline specifications

Software tools FieldTrip, NeuroScope, Klusters, CircStat
Applications Miscellaneous, Clinical electrophysiology
Organisms Rattus norvegicus