Computational protocol: Basal Forebrain Activation Enhances Cortical Coding of Natural Scenes

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Protocol publication

[…] Local field potential analysis was carried out using Gabor/Morlet wavelet decomposition ( For single unit isolation, polytrode contact sites (channels) were separated into groups (2–4 channels per group) and spike waveforms were sorted using NeuroScope (, NDManager (, and Klusters ( In some instances, a single neuron was picked up by more than one electrode group. To ensure that duplicate neurons were not included in the subsequent analyses, pairwise between-neuron correlation coefficients (CC; binned at 1000 Hz) were calculated following clustering; for any pair with CC > 0.1, the cell with lower firing rate was discarded. For the remaining single units, only those with firing rates > 0.5 spikes s−1 were included in further analyses, performed in MATLAB (The Mathworks).For calculation of between-cell and between-trial CC ( and ), firing rates were binned at 10 Hz (although results were similar for binning from 5 Hz to 25 Hz). To determine whether a given cell was visually driven, we compared the average between-trial CC within movies and between movies. Only cells that had significantly higher within-movie CC (threshold α = 0.01, Wilcoxon signed-rank test) were included in further analyses. The burst-tonic ratio was calculated by measuring the number of burst spikes (two or more spikes occurring with ISI < 4 ms following an absence of spiking for > 100 ms) relative to the number of tonic spikes (all spikes not meeting the burst criteria).To quantify the ON and OFF receptive fields measured with sparse noise ( online), each receptive field was fitted with a two-dimensional Gaussian function:where R(x,y) is the response at pixel position (x,y), a0 is the DC component, a is the receptive field peak amplitude, (x0,y0) is the receptive field center, and σM and σm are the standard deviations along the major and minor axes. The receptive field size is measured by πσMσm, and the amplitude/baseline ratio is measured by a/a0.To measure orientation tuning and direction selectivity ( online), firing rate as a function of orientation was fitted as the sum of two Gaussians with peaks 180° apart:where R(θ) is the response at orientation θ, a0 is the DC component, a1 and a2 are the amplitudes of the two Gaussians, θ0 is the preferred orientation, and σ is the standard deviation. Tuning width is measured by σ, and direction selectivity is measured by [R(θ0)−R(θ0+180°)]/[R(θ0)+R(θ0+180°)].For the discrimination analysis (), the responses were also binned at 10 Hz. For each discrimination, the single-trial response in a given bin (Ai, where i is the trial number) was compared to the mean responses (averaged across trials) in the same bin () and in a different bin () based on the Euclidian distances d(Ai, ) and d(Ai, ). The classification was considered correct if d(Ai, ) < d(Ai, ), and incorrect if d(Ai, ) > d(Ai, ). Discrimination performance was assessed by the percentage of correct classifications for all the trials. Since the discrimination performance is expected to increase nonlinearly with the number of neurons, it is difficult to measure the redundancy between neurons. We thus converted the discrimination performance into a measure of information as I = 1 + (p)log2(p) + (1−p)log2(1−p)), where p is the discrimination performance (note that when discrimination is at chance level, p = 50%, I = 0). This definition of I represents the mutual information between the actual stimulus and the stimulus decoded from the neuronal response by the ‘ideal observer’ in the discrimination analysis. I(N) is computed as the average information across all combinations of N simultaneously recorded cells in each experiment, and it should increase linearly with N if there is no redundancy between neurons. Downward deviation from the diagonal line in thus reflects the degree of redundancy. For population analyses (), only experiments with ≥ 15 simultaneously recorded single units were included (12/19 experiments).To test statistical significance, Wilcoxon signed-rank test was used for paired samples and Wilcoxon rank-sum test was used for unpaired samples; multiple comparisons were corrected with the Bonferroni method. […]

Pipeline specifications

Software tools NeuroScope, NDManager, Klusters
Application Clinical electrophysiology
Organisms Rattus norvegicus
Chemicals Acetylcholine