lang.: Programming language, # elect.: Maximum number of electrodes tested on, data preproc.: Data preprocessing (formatting, filtering, artefact removal) included, event/channel loc.: Localization of single events, waveform extrac.: Spike features (such as peak to peak distance and full-width half max) are extracted from waveforms, e/i sorting: excitatory and inhibitory cell sorting, validation: validation of cell-type sorting (+) = ground truth validation via intracellular recordings, but not e/i validation, experim. prot.: integrates an experimental protocol to allow for network manipulation, unsuper.: unsupervised, requiring no manual user-intervention, source code available: entire code is open-source and available.

Workflow diagram of the proposed method.

(A) Filtering of the data is achieved through bandpass filtering (300 to 5000 Hz). Spike detection is done on filtered voltages, however raw voltages around each spike to avoid signal distortion. (B) Spike sorting on each electrode. (Bi) Events are detected using a threshold method (6 SD from the mean of the filtered signal). (Bii) PCA and k-means on individual waveforms (k = 2) (C) Precise soma location on the array. (D) Excitatory and inhibitory sorting. (Di) Spike time constants kinetics are extract at the full width at half maximum and peak to peak distances. (Dii) Interpolated voltage for increased resolution (Diii) k-means to distinguish cell-type based on their waveform kinetics.

Isolation of single-cell action potential for each electrode.

(A) Multielectrode array recording set up (B) Extracellular voltage on a single electrode (Bi) Spike detection on filtered voltage (Bii) Raw voltage extraction around detected spike (C) Firing rate per electrode depends on threshold selection. Inset shows firing rate values at the selected threshold (4 SD) D) Threshold selection to part cellular activity from normally distributed noise (E) Spike sorting on a single electrode (F) Current sink signal from single neuron spans multiple electrodes (4 different neurons are shown in different colors) (G) Histogram distribution of ten-fold cross-validation with chance performance indicated in red for all electrodes in a single recording. (H) Voltage amplitude as a function of distance from highest electrode peak, inset shows the directions measured from the center electrode(I) Center of mass location of all spikes for a single soma, mean is indicated in red.

Identification of putative excitatory and inhibitory units.

(A) Distinct waveform kinetics for E and I cells (B) Respective cell location (C) Raster plot of E and I activity. (D) Fano factor for putative E and I cells. The shaded area represents the standard error of the mean (SEM).The x-axis shows temporal bins of increasing durations employed to compute the fano factor (E) Mean cross-correlation as a function of spatial distance between pairs of electrodes. Non-overlapping bins of 100 ms were employed to compute correlations. The resulting values were averaged by spatial distance between all pairs of neurons.

Validation of step-function opsin by whole-cell recordings.(A) Visually identified PV neuron (B) Nearby pyramidal neuron receiving inhibitory currents following PV opto activation (C) IPSCs onto pyramidal cell with 20 s rest between trial (D) IPSCs onto pyramidal cell with 60 s rest between trial (E) IPSCs onto pyramidal cell with 120 s rest between trial

Optogenetic targeting of inhibitory cells for spike sorting.

(A) Average firing rate for putative excitatory and inhibitory neurons. The shaded area represents the SEM. (B) Quantification of change in firing rate in panel A (C) Delta change in firing rate (on – drugs) (D) Opto-evoked change in firing rate

Light artefact in a recording from mouse prefrontal cortex showing that the application of a brief (1 ms) pulse of light leads to saturation lasting about 5 ms post-stimulation.