Fig. 9: Neuropixels CMOS shanks resolves spiking and LFP in the z-plane of a whole brain organoid.

a A Neuropixels high-density CMOS shank was attached to a custom-made mount and controlled by a micromanipulator in order to lower the shank into an immobilized brain organoid kept at 37 °C in BrainPhys media. b Left, spikes (above a 5-rms threshold) were detected in a subset of electrodes near the tip of the shank. Spike activity is normalized relative to the electrode with the most detected spikes. Top right, raster-plot visualization of single-unit spiking activity (Kilosort2) as shown by the blue dots for each sorted unit. Stereotyped population bursts are visualized as peaks in the population averaged firing rate (red line). Bottom right shows the extracellular field potentials (0.3–4 kHz) generated by a spiking neuron within the organoid as measured by the shank. c Top, spectrogram plot of local field potential (LFP) from an electrode illustrates dominant oscillation power in the theta and delta bands. Bottom, raw LFP (gray line) from the same electrode overlaid with the theta-filtered band (red line). d Theta phase traces (gray lines) are shown relative to population burst peak events (red dotted line) reveal phase coherence as illustrated by a drop in the phase angle spread plotted in radians (blue line). The bottom plot shows an electrode site displaying no phase coherence relative to population burst events. e Left, spatial map of the change in theta phase angle spread is shown relative to burst peak time across the shank. The bubble size indicates the inverse of the phase angle spread relative to the burst peak for each electrode. Notice the overlap with phase coherent sites and the spatial region registering spiking activity on the right. f Left, circular distribution of theta-spike phase angles measured from a single electrode site. The direction of the mean spike angle (µ) relative to the theta phase and magnitude (mean resultant length) are shown as polar plots. The Rayleigh criteria for non-uniformity was used to determine if spikes were distributed non-uniformly over the theta cycle (0°, 360°). Right, distributions of theta-spike angles shown relative to the theta cycle. g Mean theta phase angle of spike phase-locked electrodes across the Neuropixels probe satisfying the Rayleigh test for non-uniformity (p < 0.05).