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Pipeline publication

[…] b'ered by a 470 nm (blue) LED (M470F1, Thor Labs, Newton NJ), and focused on a circular area of ~1 mm2 centred on the silicon probe insertion site., To estimate the proportion of recorded neurons directly activated by ChR2, we performed a control experiment, in which 20 and 40 Hz trains of five 2 ms pulses of ~100 mW/mm2 intensity were delivered to the silicon probe insertion site using a MBL-III-473nm-150mW blue light laser (CNI, Chungchun China). Reliable, short latency (< 5 ms) and low jitter (< 1 ms) responses were found in ~5% of the units, indicating that ~95% of cells were driven polysynaptically rather than directly., Spikes were detected and visually verified using the programs NDmanager and Neuroscope. Spike sorting involved an automated stage, performed using KlustaKwik, and a manual verification stage for which Klusters or KlustaViewa were used. Detailed analysis of coupling to population rate and LFP was performed only for units with isolation distance > 20 (see refs. ,). Units were selected and sorted blind to measures of population coupling and all other cellular parameters., Population rate (e.g. in ) was computed by accumulating all the detected spikes (both well-isolated units and multi-unit activity) with 1 ms resolution, and smoothing the resulting vector with a Gaussian of half-width 12 ms. The population rate used to compute the stPR for any individual unit did not include the spikes of that unit. The baseline level of each stPR (which reflects the mean population rate) was subtracted.' […]

Pipeline specifications

Software tools NDManager, NeuroScope, Klusters