Single-neuron perturbations reveal feature-specific competition in V1

Abstract

The computations performed by local neural populations, such as a cortical layer, are typically inferred from anatomical connectivity and observations of neural activity. Here we describe a method-influence mapping-that uses single-neuron perturbations to directly measure how cortical neurons reshape sensory representations. In layer 2/3 of the primary visual cortex (V1), we use two-photon optogenetics to trigger action potentials in a targeted neuron and calcium imaging to measure the effect on spiking in neighbouring neurons in awake mice viewing visual stimuli. Excitatory neurons on average suppressed other neurons and had a centre-surround influence profile over anatomical space. A neuron's influence on its neighbour depended on their similarity in activity. Notably, neurons suppressed activity in similarly tuned neurons more than in dissimilarly tuned neurons. In addition, photostimulation reduced the population response, specifically to the targeted neuron's preferred stimulus, by around 2%. Therefore, V1 layer 2/3 performed feature competition, in which a like-suppresses-like motif reduces redundancy in population activity and may assist with inference of the features that underlie sensory input. We anticipate that influence mapping can be extended to investigate computations in other neural populations.

Extended Data Figure 1:

Photostimulation characterization and methods (a) Left, images showing GCaMP6s and densely expressed, soma-localized C1V1 in the same neurons. Right, an image of Channelrhodopsin-2 tagged with mCherry, obtained from a different mouse. Note that non-localized channels are prominent in the neuropil background compared with soma-localized channels. (b) Photostimulation protocol schematic. Top: beam position as a function of time, samples of mirror trajectory plotted at 100 kHz. Bottom: Four repeats of an identical sweep were used to photostimulate neurons. (c) Photostimulation triggered average images, for a neuron (left) and control (right) site from the experiment in Fig. 1b. Arrows mark the location of both sites. (d) Cumulative density plots of photostimulated neuron responses for different lateral displacements of target location from the neuron’s center. Same data as in Fig. 1e, but note log scale of x-axis. The 15-25 μm offset caused responses that were not present at greater distances. (e) Fraction of neurons that could be photostimulated as a function of the threshold for this classification. At a threshold of 5 std above shuffle, more than 96% of neurons (n=518) could be photostimulated. Shuffle distributions were computed by bootstrap resampling of activity from trials the neuron was not targeted. (f) Fit quality of the GP tuning model vs. photostimulation magnitude. Each dot is a single targeted neuron (n = 518 neurons). Spearman correlation, c = 0.084, p = 0.055. (g) Mean gratings response of a neuron vs. photostimulation magnitude. Each dot is a single targeted neuron (n = 518 neurons). Spearman correlation, c = 0.11, p = 0.009. (h) A CNN was trained with human-labeled data to predict whether CNMF sources were identified as a cell body or an alternative source, including distinct neural processes, excessively blurry or out-of-plane cells, or artefactual sources (see Methods). Note that many non-soma sources exhibited similar calcium transient signals as cell body sources. Because there is no objective ground-truth for this classification, held-out datasets were hand labeled, and compared to CNN labeling. One example dataset is shown here. The large majority of sources were labeled identically, however there are borderline cases where labels differed; many cases appear to be either human error in labeling, due to finite human time and inconsistencies in making borderline judgments, or an overly conservative CNN criteria for cell classification. Neither of these errors are expected to impact results presented in this manuscript.

Extended Data Figure 2:

Influence measured as probability excited/inhibited (log-odds excited). (a) Log-odds excited metric. This metric uses a non-parametric bootstrap procedure to estimate the chance of observing average responses to photostimulation of a target from random sampling of a neuron’s activity (see Methods). An influence value of 0.1 corresponds to a log-odds of ~1.259, or a probability of being excited above shuffles of ~0.557. This metric adapts to the varyingly sparse, heavy-tailed, and skewed response distributions of each neuron’s activity, and so complements the ΔActivity measure. Key analyses from Fig. 2 and Fig. 3 were repeated using this log-odds metric. (b) Calculation of influence using the activity of a non-targeted neuron. Examples are shown for two pairs of neurons. Left: Deconvolved activity of a non-targeted neuron on trials photostimulating a different neuron (red). Black lines indicate 5% and 95% bounds from resampling all trials. Data were smoothed with a 67 ms std gaussian filter for display only. Right: Mean deconvolved activity for non-targeted neuron averaged over 0.367 s following photostimulation of target (red). Probabilities for obtaining a given deconvolved activity from the shuffle distribution of the non-targeted neuron are shown (black). (c) Influence bias (average of signed influence values) as a function of distance between the targeted site and non-targeted neurons., plotted for both neuron and control photostimulation targets. Shading is mean ± sem. Same pairs as Fig. 2g, n = 153,689 neuron site pairs, 90,705 control site pairs. (d) Influence magnitude measured as the absolute value of influence values for all pairs following neuron or control site photostimulation. The non-zero value for control sites is expected because of noise due to random sampling of neural activity and potential off-target effects. Error bars indicate mean ± sem. n = 153,689 neuron site pairs, 90,705 control site pairs. Neuron vs. control: p = 2.31 × 10⁻⁵, Mann-Whitney U-test. (e) Influence bias for a single-target was the mean of influence values for the targeted neuron across all non-targeted neurons. Error bars indicate mean ± sem across targets. n = 518 neuron targets, 295 control targets. p = 7.40 × 10⁻⁴, Mann-Whitney U-test. (f) Influence dispersion for a single-target was the standard deviation of influence values for the targeted neuron across all non-targeted neurons. Error bars indicate mean ± sem across targets. n = 518 neuron targets, 295 control targets. p = 2.3 × 10⁻⁶, Mann-Whitney U-test. (g) The mean influence for all values for a single-target was calculated. Plotted is the standard deviation of these values for neuron sites and control sites. The similar values indicate that it is unlikely that some neurons tended to have much larger positive or negative influence than expected based on control sites. n = 518 neuron sites, 295 control sites. p = 0.88, two-sample F-test. (h) Running average of influence with noise correlation, for nearby (black) or distant (gray) pairs, with bin half-width of 20% (percentile bins). (i) Running average of influence with signal correlation, with bin half-width of 15% (percentile bins). (j) Running average of influence with difference in preferred orientation, with bin half-width of 12.5 degrees. (k) Coefficient estimates for linear regression of influence values. Plots show bootstrap distribution with median estimate as gray line, 25–75% interval as box, 1–99% interval as whiskers. Left: coefficients for piece-wise linear distance predictors from the model. Significance estimated by bootstrap: 25–100 μm, offset p = 0.0006, slope p < 1×10⁻⁴; 100–300 μm, offset p < 1×10⁻⁴, slope p < 1×10⁻⁴; > 300 μm, offset p = 0.68, slope = 0.056. Right: coefficients for activity predictors from the same model. Signal correlation, p = 0.0002; signal-distance interaction, p = 0.96; noise correlation p = 0.0010; noise-distance interaction, p = 0.0024; signal-noise interaction p = 0.14; n = 64,485 pairs. (l) Coefficient estimates from separate models in which the specified tuning correlation replaced signal correlation in the influence regression model of (i). Same bootstrap and boxplot convention as (i). Each model used only pairs in which targeted and non-targeted neurons exhibited tuning. Direction, p = 0.21, n = 36,565 pairs; orientation, p = 0.0026, n = 36,565; spatial frequency, p = 0.30, n = 47,810; temporal frequency, p = 0.011, n = 26,526; running speed, p = 0.11, n = 46,634.

Extended Data Figure 3:

Extended comparison of photostimulation of neuron sites and control sites. (a) Influence bias (mean ΔActivity) comparison between neuron and control site photostimulation, after exclusion of pairs with individually significant influence values. Significance of each individual pair’s influence was determined with a non-parametric bootstrap (Extended Data Fig. 3, Methods), and a p-value threshold for significance was chosen to restrict the fraction of false positives below 5% or 25% (pFDR, Methods). For 0%, n=153,689 neuron and 90,705 control pairs. 225 neuron and 26 control pairs were excluded for 5% pFDR, 638 neuron and 50 control pairs were excluded for 25% pFDR. Influence following neuron photostimulation was significantly negative for all thresholds, Mann-Whitney U-test, 0% p = 8.90 × 10⁻¹⁶, 5% p = 7.24 × 10⁻¹⁵, 25% p = 5.72 × 10⁻¹². (b) As in (a) but for influence dispersion (std of ΔActivity). Influence dispersion was greater following neuron than control photostimulation for all thresholds, two-sample F-test, 0% p = 6.84 × 10⁻³⁹, 5% p = 6.04 × 10⁻²⁰, 25% p = 2.63 × 10⁻¹⁴. (c) As in (a-b), but for influence bias as a function of distance. A quantitatively similar center-surround pattern was observed for all thresholds. (d) Average influence values for a non-targeted neuron (over all photostimulated neurons) vs. that neuron’s average deconvolved activity during non-photostimulated trials in influence mapping blocks. Each dot is a single non-targeted neuron. n = 8552 neurons. Spearman correlation, c = −0.00003, p = 0.99. (e) Same as in (c), except for mean trace correlation during tuning measurement blocks. c = 0.0068, p = 0.53. (f) Same as in (d), except for trace correlation strength. c = 0.0099, p = 0.36. (g) Same as in (d), except for gratings response. c = 0.0092, p = 0.38. (h) Same as in (d), except for GP tuning model fit quality. c = 0.011, p = 0.29. (i) The mean influence for all values for a single-target was calculated. The standard deviation of these values for neuron sites and control sites is plotted. The similar values indicate that it is unlikely that some neurons tended to have much larger positive or negative influence than expected based random sampling of the group mean (which was lower for neuron than control sites, see Fig. 2). Error bars, mean ± sem across targets. n = 518 neuron targets, 295 control targets, p = 0.72, two-sample F-test. (j) Running average of influence with pairwise distance using bin half-width of 30 μm. Shading corresponds to mean ± sem calculated by bootstrap. Data are divided into influence from photostimulation sites with stronger versus weaker direct photostimulation responses in the targeted neuron, using a median split of photostimulation significance, as well as for control site photostimulation. Mean photostimulation response was 0.36 ΔF/F and 0.85 ΔF/F for weak and strong groups. Note the weak distance-dependence observed for control site photostimulation is consistent with greatly reduced, but non-zero, neural excitation when targeting control sites. This may result from a number of factors including suboptimal resolution and brain movement in vivo, and indicates the necessity of control site photostimulation.

Extended Data Figure 4:

Characterizing neural tuning in V1 using Gaussian process (GP) regression. (a) GP model fit quality (pearson correlation with held-out data). Each neuron plotted at its relative position in an individual experiment’s field-of-view. Neurons at all positions were similarly well fit. (b) Two-dimensional histogram of GP model fit quality (‘test accuracy’) and prediction quality on not-held-out data (‘train accuracy’). Major overfitting was not observed. (c) Depth-of-Modulation (see Methods) for each individual tuning dimension, for all neurons that passed model fit criteria. Dimensions exhibited qualitatively distinct distributions. Left: many neurons had almost no drift direction modulation, with many others exhibiting extremely pronounced modulation (> 10). Right: Almost all neurons exhibited a moderate degree of modulation (~5) by the mouse’s running speed. (d) Z-scored tuning curves for each individual tuning dimension, for all neurons passing model fit criteria and with significant modulation (> 2) for the plotted dimension. Tuning was qualitatively different for different dimensions. Spatial frequency tuning was distributed evenly over our stimulus set and generally bandpass. Running speed tuning was distributed more tightly into a few neurons preferring stillness, versus many broadly preferring running. (e) Significance of tuning for each dimension as determined by GP regression.

Extended Data Figure 5:

Comparison of GP tuning model and conventional parametric tuning model. (a) Model fit qualities for an example session, assessed on left-out data. Each dot is a single neuron, n = 358 neurons. GP model fit qualities were higher than those from the parametric tuning model, mean difference of 0.11, p = 5.02 × 10⁻⁶⁰, Mann-Whitney U-test. (b) Estimated preferred orientations of neurons were similar between models. Pearson correlation c = 0.88, calculated using only neurons significantly tuned to orientation. (c) Estimated spatial frequency preferences of neurons were similar between models, c = 0.95 calculated using only neurons significantly tuned to spatial frequency. (d) Signal correlations calculated from the two models were similar, c = 0.80. (e) Noise correlations calculated from the two models were similar, c = 0.94.

Extended Data Figure 6:

Influence regression separates contributions of correlated similarity metrics (a) Probability density functions estimated by kernel smoothing for distance (left) and signal correlation (right), for all data used in influence regression (n = 64,485 pairs). Separate densities were estimated for pairs exhibiting varying trace correlation (left) or noise correlation (right). The plots show that pairs with high trace correlations occurred at all distances, but more often for nearby neurons. Similarly signal correlations for pairs with high versus low noise correlations were distinct but overlapping distributions. This highlights the importance and feasibility of influence regression to disambiguate the contributions of distance, signal, and noise correlation. (b) Two-dimensional probability density functions for pairs of similarity metrics, estimated using kernel smoothing, for all data used in influence regression. Spearman correlation values for each pair of similarity metrics are overlaid. All correlations were significant with p < 1×10⁻⁶⁰, n=64,845 pairs. (c) Running average of influence data (black) and predictions (colored lines) from influence regression model, using a bin half-width of 15% (percentile bins). Dashed lines are mean ± sem of data by bootstrap. Signal correlation is plotted against mean influence, for the subset of pairs more than 300 μm apart. Model predictions are computed using a full influence regression model (blue), or using subsets of coefficients from the same model (distance-red, signal-green, noise-purple). The full model prediction is equal to the sum of the three components. The running average analysis here accurately reflects the signal component of the influence regression model, plus a tonic offset from the distance component. (d) Running average as in (a), but for noise correlation and pairs at all distances. Note that signal and noise interaction coefficients with distance are included in signal and noise components, respectively. The running average analysis here confusingly indicates a flat slope of noise correlation and influence. Our model predicts this relationship because pairs with higher noise correlations were located at shorter distances, and also had increased signal correlations, and these effects together canceled out increases in influence due to noise correlation. (e) Running average as in (a), but for model-free correlations of single-trial responses, and for pairs separated by less than 125 μm. At short distances, the positive effect of noise correlations dominated the negative effect of signal correlations. (f) Running average as in (a), but for model-free correlations of single-trial responses, and for pairs separated by more than 125 μm. At long distances, the negative effect of signal correlations dominated the positive effect of noise correlations.

Extended Data Figure 7:

Results of influence regression are robust to potential artifacts from data processing and off-target photostimulation (a) Analysis of influence effects directly in ΔF/F traces. ΔFluorescence was calculated as for ΔActivity, but using ΔF/F traces rather than trial-averaged deconvolved activity. ΔFluorescence was significantly negative in the 1 s following neuron photostimulation relative to control, n = 153,689 neuron site pairs and 90,705 control site pairs. Neuron vs. control site: p = 6.79 × 10⁻¹⁵, Mann-Whitney U-test. Shading for all plots is mean ± sem calculated by bootstrap. (b) ΔFluorescence in non-targeted neurons following photostimulation of neurons at varying distances. n = 1,822 near pairs, 35,541 mid-range pairs, 35,882 far pairs. Near vs. mid-range: p = 7.62 × 10⁻¹⁹; near vs. far: p = 5.0 × 10⁻⁶; mid-range vs. far: p = 1.21 × 10⁻⁴⁷, Mann-Whitney U-test. (c) As in (b), but without neuropil subtraction, or any source de-mixing from CNMF; traces were extracted by projecting raw movies onto neuron ROIs. n = 1,822 near pairs, 35,541 mid-range pairs, 35,882 far pairs. Near vs. mid-range: p = 5.96 × 10⁻²⁸; near vs. far: p = 5.21 × 10⁻³⁸; mid-range vs. far: p = 4.15 × 10⁻¹³, Mann-Whitney U-test. This indicates that distance-dependent influence effects were not an artifact of source extraction algorithms. (d) The influence regression from Fig. 3d was applied to ΔFluorescence traces. This regression resulted in beta coefficients for traces at each time frame relative to photostimulation onset, which are plotted over time. Coefficients for slopes for the three distance bins are plotted. The same size and ordering of effects is apparent as when using deconvolved data and the ΔActivity metric, compare to Fig. 3. Shading corresponds to mean ± sem, calculated using 10,000 coefficient estimates by bootstrap resampling. All coefficients were significantly different from zero, averaged over 0–1,000 ms from photostimulation onset, with p < 1×10⁻⁴ by bootstrap. (e) Same as in (a) except for signal and noise correlation coefficients. Averaged over 0–1,000 ms from photostimulation onset, signal correlation coefficients were significantly less than zero with p = 0.0008 and noise correlation was greater than zero with p = 0.0154, estimated by bootstrap. (f) Similar to regression analysis in Fig. 3d–e, except as a test of potential off-target effects. Instead of using only the photostimulated neuron’s activity and tuning properties to calculate correlations with the non-targeted neuron, properties of multiple nearby neurons were used, to test if off-target photostimulation of nearby cells could underlie the observed effects (see Methods). This is equivalent to influence regression using identical influence values and distance predictors as in Fig. 3e, but changing all activity predictors. Only distance effects were apparent, as expected, whereas activity-related effects were absent. This suggests that the properties of the individually targeted neuron were responsible for the influence relationships we observed. Plots show bootstrap distribution with median estimate as gray line, 25–75% interval as box, 1–99% interval as whiskers. Left: coefficients for piece-wise linear distance predictors from the model. Significance estimated by bootstrap: 25–100 μm, offset p = 0.0982, slope p < 1×10⁻⁴; 100–300 μm, offset p < 1×10⁻⁴, slope p < 1×10⁻⁴; > 300 μm, offset p = 0.0018, slope = 0.0316. Right: coefficients for activity predictors from the same model. Signal correlation, p = 0.9370; signal*distance interaction, p = 0.4072; noise correlation p = 0.8772; noise*distance interaction, p = 0.5138; signal*noise interaction p = 0.5260; n = 64,485 pairs.

Extended Data Figure 8:

Population analysis of gratings responses during influence mapping blocks (a) The orientation information content of all neurons during influence mapping blocks, calculated using the same binning approach used for population decoding. Information is color coded, and plotted as a function of a neuron’s directional modulation and preferred spatial frequencies estimated during tuning measurement blocks. This demonstrates that tuning estimated in tuning and influence measurement blocks were concurrent (gratings during influence mapping were always 0.04 cyc/deg), but that responses to full-field, low-contrast gratings in influence measurement blocks were sparse. (b) Schema indicating the orthogonalization procedure used for population analysis. Briefly, because average responses to each grating orientation were not entirely orthogonal, and because photostimulation evoked highly significant changes in response gain in our dataset, we wished to isolate potential changes along alternative population activity dimensions independent of gain changes. To accomplish this we orthogonalized projections along non-gain dimensions relative to the gain projection observed on individual trials. This ensured that changes in response gain could not trivially produce changes along non-gain population dimensions.

Extended Data Figure 9:

‘Toy’ model of feature competition and its functional implications. (a) Diagram of rate-network model, in which each neuron i receives feedforward input u_i driven by the orientation of a visual stimulus and has functional connection w_i,j with neuron j. Neurons were modeled as rectified-linear units. (b) Influence regression coefficients for the rate-network model. Signal and noise correlations were estimated from noisy simulated trials and regressed against functional connections W, similar to Fig. 3d–e. To be consistent with experimental data, random trial-to-trial fluctuations in gain as well as single-neuron-specific noise were added to simulations (see Methods), such that all networks exhibited a positive correlation between signal and noise correlations. However results were similar without simulated gain fluctuations. (c) Model neuron responses following presentation of a 90 degree stimulus. Feedforward inputs were identical for all networks. Colors are the same as in panel (a). Dashed line indicates orientation of the visual stimulus. (d) Model neuron responses following presentation of a linear sum of 60 and 120 degree stimuli. Gray lines are the average response of each network to the two stimuli presented individually. Note that neurons preferring 70 and 110 degrees receive the maximum feedforward input. (e) Model neuron responses to a visual stimulus (90 degrees) with simulated photostimulation of a neuron. Responses (in non-stimulated neurons) are shown when the “photostimulated” neuron had preference for similar (top, 80 degrees) or dissimilar (bottom, 10 degrees) orientations relative to the visual stimulus, color coded by network type. Responses are normalized to activity without simulated photostimulation. (f) Model network responses to visual stimuli with simultaneous “photostimulation”, as a function of difference in orientation between visual stimulus and “photostimulated” neuron’s preference. The response gain dimension was calculated as the normalized response to the visual stimulus in the absence of “photostimulation”. (g) Analytical solution for the linear aspect of network dynamics (see Methods for derivation). This indicates that the network performs a comparison between inputs y and an internal estimate y^net, which when s is negative corresponds to dynamical explaining away of network inputs.

Extended Data Figure 10:

Interaction of trace correlation with influence regression model coefficients (a) Further characterization of the effects of trace correlation on feature competition vs. amplification (compare to Fig. 5d). Influence regression (as in Fig. 3d) was performed after including an interaction of each predictor with the magnitude of trace correlation. Coefficient estimates for each interaction plotted with uncertainty from bootstrap: gray line, median; box, 25–75% interval; whiskers, 1–99% interval. This analysis used no manually-specified division between ‘strong’ and ‘weak’ correlations, and considered whether trace correlation changed the relationship between influence and any predictors in the influence regression. Signal correlation exhibited a highly significant positive interaction, indicating a transition from competition (negative slope) to amplification (positive slope) as the magnitude of trace correlation increased, n = 64,845 pairs, p = 0.0002 (bootstrap). Interactions with all other activity predictors were not significant with p > 0.444. Interactions with the slopes of distance predictors were not significant with p > 0.2716. There were weak interactions with offsets for near (p = 0.0486) and mid (p = 0.0076) distance bins, but not far (p=0.4738). These results indicate that the magnitude of trace correlation had a substantial effect on the relationship between signal correlation and influence.

Figure 1:

Photostimulation of targeted neurons (a) Influence mapping schematic. (b) Example field-of-view with neuron (red) and control (blue) photostimulation sites. (c) Top: Tuning blocks measured responses to drifting gratings with varying direction, spatial frequency, and temporal frequency. Bottom: Influence blocks presented 10% contrast visual stimuli simultaneous to single-neuron photostimulation. (d) Photostimulation-triggered average fluorescence changes from raw images centered on targeted neuron sites (n = 31) and control sites (n = 10). n = 153 trials per site. (e) Left: Photostimulation sites (colored circles) near isolated C1V1-expressing neuron. Right: Fluorescence transients following photostimulation at sites in left panel. (f) Response vs. distance between centers of photostimulation and soma (normalized by median at > 65 μm). n = 9 experiments, 3 mice, 98 targets at 16,019 sites, 25 trials/site. Compared to > 65 μm (n = 13,367 sites): p < 1.3 × 10⁻³ for each bin ≤ 15-25 μm (n = 774); p > 0.17 for each bin ≥ 25-35 μm (n = 300), Mann-Whitney U-test. (g) Left: Activity traces during tuning and influence blocks. Red dots mark photostimulation times. Right: Single-trial traces for all photostimulation events during an influence block (smoothed for display). Black lines, mean. (h) Responses to optimal visual stimuli during tuning block (green) and to visual stimuli during influence block with (red) or without (blue) photostimulation. Influence block with photostimulation vs. optimal visual stimulus: p < 3.1×10⁻⁶, Mann-Whitney U-test, n=518 neurons. (i) Example cell-attached electrophysiology during photostimulation. Left: Cell recorded and targeted for photostimulation, white arrow. Middle: Single trial trace during photostimulation. Right: Raster plot of spikes across all trials. Photostimulation (red): four 32 ms-long sweeps at 15 Hz. (j) Spikes added over four photostimulation sweeps in ~250 ms. Mean ± sem: 6.38 ± 1.01 spikes added per trial. n = 9 cells.

Figure 2:

Measurement and characterization of influence (a) Left: calculation of ΔActivity: activity in a non-targeted neuron on single trials following photostimulation of neuron site 1 (red) and on control trials (blue) with matched visual stimulus (gray box). x_t, values for all trials with photostimulation of site t. Center, Right: ΔActivity and traces for example pairs. Traces smoothed for display, shading is mean ± sem (b) Photostimulation-triggered average fluorescence changes from raw images centered on all non-targeted neurons for pairs with ΔActivity > 0.15 (left) or < −0.15 (right). (c) Influence magnitude (average of |ΔActivity| values) following neuron site (n = 153,689 pairs) or control site (n = 90,705) photostimulation. The non-zero value for control sites is expected because of noise due to random sampling of neural activity and potential off-target effects. Error bars, mean ± sem calculated by bootstrap. Neuron vs. control: p = 1.23 × 10⁻¹⁹, Mann-Whitney U-test. (d) Influence bias (average of signed ΔActivity values) for a single target was the mean ΔActivity across all non-targeted neurons. Error bars, mean ± sem across targets. n = 518 neuron targets, 295 control targets. p = 0.0023, Mann-Whitney U-test. (e) Same as for (d), except for influence dispersion for a single target, which was the standard deviation of ΔActivity across all non-targeted neurons. p = 2.1 × 10⁻⁶, Mann-Whitney U-test. (f) Influence magnitude vs. distance between the target site and non-targeted neuron for pairs with neuron site (n=153,689) or control site (n=90,705) photostimulation, shading is mean ± sem (g) Influence bias vs. distance, as in (h).

Figure 3:

Relationship of influence to activity similarities between neurons (a) Tuning for spatial frequency and direction for a pair of neurons. Each dot is a single trial color-coded by the mean activity throughout the visual stimulus. Data (top) and GP model predictions on held-out trials (bottom) showed high correspondence. (b) One-dimensional tuning curves for the pair in (a), predicted from the GP model. Shading, mean ± sem. (c) Signal correlation (left), noise correlation (middle), and trace correlation (right) for the pair in (a-b). (d) Design of influence regression. Predictors were z-scored so that coefficients indicate the change in influence for 1std increase in predictor. (e) Influence regression coefficient estimates based on bootstrap. Gray line, median; box, 25-75% interval; whiskers, 1-99% interval. Left: piece-wise linear distance predictors. 25-100 μm, offset p=0.048 (bootstrap), slope p<1×10⁻⁴; 100-300 μm, offset p<1×10⁻⁴, slope p<1×10⁻⁴; >300 μm, offset p=0.009, slope p=0.078. Right: activity predictors from the same model. Signal correlation, p=0.0004; signal*distance, p=0.77; noise correlation p=0.0024; noise*distance, p=0.013; signal*noise, p=0.17; n=64,485 pairs. (f) Coefficient estimates from separate models, based on (d), using the specified correlation instead of signal correlation and pairs in which both neurons exhibited tuning. Direction, p = 0.18, n = 36,565 pairs; orientation, p = 0.0058, n = 36,565; spatial frequency, p = 0.32, n = 47,810; temporal frequency, p = 0.020, n = 26,526; running speed, p = 0.41, n = 46,634. (g) Influence vs. noise correlation, for nearby (black, n=8,538) or distant (gray, n=56,307) pairs. Percentile bins, 20% half-width. Similar results with different distance thresholds (not shown). Shading, mean ± sem calculated by bootstrap. (h) Influence vs. signal correlation. Percentile bins, 15% half-width. (i) Influence vs. difference in preferred orientation. Bin half-width, 12.5 degrees.

Figure 4:

Effects of feature competition on population encoding of orientation (a) Naïve-Bayes decoding of orientation from population activity during influence blocks. Error bars, mean ± sem, logistic regression mixed-effects model, non-overlapping bins. Line, logistic regression on non-binned data with a continuous similarity predictor; p = 0.00056, n = 54,187 trials, F-test. (b) Population activity (deconvolved ΔF/F) along dimension for 0-degree oriented stimuli on control trials, example experiment. Activity along this dimension was high only during 0-degree stimuli, showing that population dimensions allow orientation discrimination. Shading, mean ± sem (bootstrap) (c) Following (b), population activity along the 0-degree dimension during a 0-degree stimulus was decreased by photostimulation of example neurons preferring a similar stimulus (10-degrees) but not neurons preferring alternate stimuli (45-degrees). (d) Following (b-c), photostimulation triggered little change along dimensions not aligned (0-degree dimension) with the presented stimulus (45-degrees). (e) Changes in population encoding as a function of similarity between the orientation of visual stimulus and a photostimulated neuron’s preference. Dots, mean ± sem for 5 non-overlapping bins; line, linear regression on non-binned data using a single continuous predictor. The population response along the dimension of presented stimulus (‘gain’ dimension) was suppressed when orientations were similar, c = 0.0115, p = 0.0076, Spearman rank correlation. n = 54,187 trials. (f) Responses along other directions were not affected, orthogonal orientation projection, c = 0.0045, p = 0.2974, n = 54,187 trials. (g) Responses along the uniform dimension were not affected, c = −0.0046, p = 0.2880, n = 54,187 trials. (h) Rate-network model. Neuron i receives feedforward input u_i and has functional connection w_i,j with neuron j. (i) Model neuron responses for a 90 degree stimulus (dashed line). Feedforward inputs were identical for all networks. (j) Model neuron responses for a linear sum of 60 and 120 degree stimuli. Gray lines, summed network response to the stimuli presented individually. Feedforward inputs have maxima ~70 and 110 degrees.

Figure 5:

Strongly-correlated pairs exhibit non-competitive influence (a) Histogram of trace correlations. (b) Influence vs. trace correlation. Bin half-width, 0.1. Right: zoom on central 95% of trace correlations. Shading, mean ± sem (bootstrap), n=153,689 pairs. (c) Signal and noise correlations colored by trace correlation. Line, average signal and noise correlations for the trace correlation bins in (b), colored by weak (central 95%) or strong (top, bottom 2.5%) trace correlations. Trace correlation is related, but not identical to, the sum of signal and noise correlations. (d) Influence regression coefficients, as in Figure 3e. All data, black; pairs with weak (gray) or strong (purple) trace correlations. Distance predictors were included (not shown, see Extended Data Fig. 10). For strong trace correlations: signal correlation, p = 0.011 (bootstrap), n = 3,242 pairs; other coefficients, p > 0.32. (e) Single trial rate-network model neuron responses to a 90 degree stimulus (left) or sum of 60 and 120 degree stimuli (right), with noisy inputs. Gray lines, responses without added noise. Black lines, feedforward inputs (without noise). (f) Cross-correlation of single-trial responses on 1000 simulated noisy trials to the noiseless response (maximum value over all shifts in orientation). (g) As in (f), but for the shift in network response due to noise in the input (orientation center-of-mass of activity relative to the noiseless response).