Cortical layers of V1.

(A) Laminar divisions of macaque monkey V1 revealed with different histological staining methods (Nissl for cell density, Anti-NeuN for neuronal density, CO for metabolic activity and VG2 for glutamatergic axon terminals). Adapted from (1). (B) Schematic diagram of V1 layers that receive different functional/anatomical types of LGN afferent input (13). LGN magnocellular (M; L+M achromatic, grey in 4Cα), parvocellular (P: L/M cone-opponent, red-green in layer 4Cβ; S-OFF, lime in layer 4A) and koniocellular (K: S-ON, purple in layer 3B CO blobs). (C) Electrode spacing and layout of Neuropixels 1.0 probe. (D) Layout of probes that were used in E and F. (E) An example of V1 CSD profile in awake recordings using a 16-channel linear probe (8). (F) Another example of V1 CSD profile in anesthetized recordings using a 24-channel linear probe (9). Supragranular (S), granular (G) and infragranular (I) layers were delineated in E and F mainly based on transitions between the short-latency granular layer sink and adjacent sources.

CSDs evoked by a black to white visual stimulus transition through the dominate eye, all targeting achromatic ON domains.

The layer boundaries drawn here were determined using the methods and data described in the subsequent sections. (A) CSD profile from the LFP traces of all contacts with 20µm depth spacing (Penetration A10). (B-D) Gaussian filtering of the CSD profile in A along the depth of probe with σ equals 20µm (B), 30µm (C) or 40µm (D). (E-H) CSD profiles from four penetrations (E: A10, F: A14, G: B12, H: B13) generated using 30µm gaussian smoothing. The CSD profiles were aligned relative to the border between L4Cβ and L5, and CSD scales were each independently color-mapped relative to the maximum absolute deviation (MAD) in each profile.

ΔCSD profiles of three penetrations (A: A14, B: B3, C: B7) under different stimulus presentations.

Square icons above CSD profiles indicate the different color transitions used to generate the CSDs, as well as which eye was stimulated. The outline of each square indicates the color of the screen before the stimulus transition at time zero, while the filled color indicates the flashed color (Achromatic, Black and White; or color pairs in DKL color space; See Method). Black and White correspond to achromatic stimuli; Red to L-ON, M-OFF; Green to M-ON, L-OFF; Purple to S-ON, (L+M)-OFF; and Lime to S-OFF, (L+M)-ON. Dashed contours (two leftmost columns) indicate visual presentation to the non-dominant eye and solid contours indicate stimuli presented to the dominate eye. Color maps for ΔCSD profiles were independently scaled according to the maximum absolute deviation (MAD) in each profile.

Unity density and spike waveforms features across cortical depth.

(A) Cell (DAPI, cyan lines) and neuron (NeuN, red lines) density distribution in V1 adapted from previous study (18). The cortical depth, i.e., distance below the pial surface, was normalized by dividing the distance from the pial surface to the white matter. The lighter, thin lines were density profiles for individual animals and bold lines show the mean of the density profiles from the three animals. (B) Unit density distribution along the probe for one penetration (A6). (C) Average spike waveform of maximum height was shown for single unit (green) or multi-unit (gray). The insets show the spike spatial spread on the Neuropixels probe for the units with corresponding color, and the filled bands indicate the upward spread (blue) and downward spread (orange). (D) Upward (blue) and downward (orange) spike spread. (E) Spike duration. (F) Spike peak-trough amplitude ratios. B-F are from the same penetration (A6). In D-F, each dot plots a unit, and lines are smoothed distributions along the probe (See Methods). The transitions to small spike spread in D, sign reversals of spike duration in E and crosses at −1 of peak-trough ratio in F, are strong indicators for the locations of the border between white matter (WM) and gray matter (GM).

Laminar power spectrum (Pf) profiles for three penetrations (A: A2, B: A3, C: B1) generated in response to different stimulus conditions.

Power spectrum profiles were independently color-mapped according to the minimum and maximum power in each profile (See Figure 3 legend for stimulus conditions corresponding to icons above plots). The green lines and corresponding shaded ribbons show the Mean±SEM power across frequency (300-3000Hz). Note that SEM is roughly the same as the thickness of the line.

Local coherence spectrum (Cf) profiles for three penetrations (A: B12, B: B10, C: B3) generated in response to different stimulus conditions.

Local coherence profiles were independently color-mapped according to the minimum and maximum local coherence in each profile (See figure 3 legend for stimulus conditions corresponding to icons above plots). The green lines and corresponding shaded ribbons show the Mean±SEM local coherence across AP frequency (300-3000Hz). Note that SEM is roughly the same as the thickness of the line.

ΔP/P profiles for three penetrations (A: A3, B: A13, C: B3) generated in response to different stimulus conditions.

ΔP/P profiles were independently color-mapped according to the maximum positive (red) and negative (blue) absolute deviation (MAD) for each profile (See figure 3 legend for stimulus conditions corresponding to icons above plots).

V1 layer delineation for an example penetration (A2) based on AP power spectrum (A), local coherence (B), instantaneous AP power changes (C), CSD changes (D), unit density (E), spike spread (F), spike duration (G) and spike peak-trough ratio (H).

Conventions are the same as for corresponding plots illustrated in earlier figures.

V1 template and average metrics across cortex.

(A) Identified layers for 31 electrode penetrations aligned to the surface of cortex. (B) V1 layer template and probability density function for the thickness of each layer, aligned on the corresponding boundaries from the layer template. (C-J) Average depth distributions from 31 electrode penetrations. (C-F) First group of identification metrics (C: unit density, D: spike spread, E: spike duration, F: spike peak-trough ratio) on the normalized layer template (gray lines for each penetration, red line and shaded ribbon for Mean±SEM). (G-J) Second group of identification metrics (G: power spectrum, H: local coherence spectrum, I: ΔP/P, J: ΔCSD) on the normalized layer template. Conventions are the same as in previous figures.

Comparing spatial averaging to downsampling for CSD profiles evoked by flipping the black screen to the white screen through the dominant eye.

The same four penetrations in Figure 2E-H are shown here (A: A10, B: A14, C: B12, D: B13). In the downsampling process, LFPs from electrodes with increasing vertical spacing (d=20, 40, 60, 80, 100µm, gray) were used to calculate CSDs, then they were interpolated (Cubic Spline) to the vertical resolution of 20µm. In the spatial averaging process, CSD profiles of 20µm spacing were Gaussian filtered with increasing width (σ=20, 30, 40µm, red). The CSD profiles were independently color-mapped according to the maximum absolute deviation (MAD) in each profile.

V1 layer delineation for example penetration (A3) based on power spectrum (A), local coherence (B), instantiations power changes (C), CSD changes (D), unit density (E), spike spread (F), spike duration (G) and spike peak-trough ratio (H).

V1 layer delineation for example penetration (B3) based on power spectrum (A), local coherence (B), instantiations power changes (C), CSD changes (D), unit density (E), spike spread (F), spike duration (G) and spike peak-trough ratio (H).

Thickness of primary visual cortex.

(A) The distance was measured from the location of penetration perpendicular to V1/V2 border. Here, all penetrations except A17 (penetration location information lost) were included. (B-D) Distributions of cortical thickness across two monkeys, different ocular dominance columns, and COFD groups. No significant differences were found in each category (Kruskal-Wallis Test, p>0.05). COFD-A: Achromatic ON/OFF domains; COFD-LM: L- and M-cone ON/OFF domains; COFD-S: S-cone ON/OFF domains.

Average Metrics in V1 template.

(A) Normalized average power for each stimulus. Gray lines are for each penetration, and red lines and shaded ribbons show Mean±SEM. (B) Normalized average local coherence for each stimulus is shown similarly to (A). (C) Normalized average ΔP/P in time window: [30, 100]ms after stimulus onset. (D) Normalized average ΔCSD in the same time window of C. The color-mapped lines and shaded gray ribbons in C and D show Mean±SEM. Square Markers are the same as in the figures of this article.

Average normalized ΔCSD of each layer for different COFDs.

Averaging was applied for each penetration (gray lines in Figure S5D). COFD groups were compared in (A), and further compared under each stimuli group in (B). Statistical significance was represented as *: p<0.05, **: p<0.01, ***: p<0.001, Mann-Whitney U Test. COFD-A: Achromatic ON/OFF domains; COFD-LM: L- and M-cone ON/OFF domains; COFD-S: S-cone ON/OFF domains.

Average metrics from gamma band LFP in V1 template.

(A-B) Average gamma band (30-100Hz) spectrum profile of power (A) and local coherence (B) across penetrations. The square markers and color bars were the same as the figures in this article. (C-D) Normalized average power and local coherence in the gamma band. Gray lines are for each penetration, color-lines and corresponding shaded ribbons show Mean±SEM.

Average metrics from baseline activity in V1 template.

(A-B) Average baseline AP spectrum profile of power (A) and local coherence (B) across penetrations. The square markers and color bars were the same as the figures in this article. (C-D) Normalized average baseline AP power and local coherence. Gray lines are for each penetration, color-lines and corresponding shaded ribbons show Mean±SEM.

AP power and local coherence averaged across frequencies for each trial.

(A-C) Powers for the same penetrations (A: A2, B: A3, C: B1) in Figure 5. (D-F) Local coherences for the same penetrations (D: B12, E: B10, F: B3) in Figure 6. Power and local coherence profiles were independently color-mapped according to the minimum and maximum in each profile. The green lines and corresponding shaded ribbons showed the Mean±SEM across trials.

Non-rigid drift correction.

(A) Probe drifting during the recording time for one penetration (B1) was visualized as average spike amplitudes shifting in consecutive batches (batch length: ∼3.3 sec).(B) Drift estimated using the default method in Kilosort 3 (drift range: [-300, 300] µm, number of blocks: 13, drift range for each block: [-300, 300] µm). (C) Expected correction result after applying (‘imwarp’ function in MATLAB) the estimated drift in B on A. (D) Drift estimated using ‘imregdemons’ function in MATLAB. (E) Expected correction result after applying (‘imwarp’ function in MATLAB) the estimated drift in D on A.