Claims 56
From the paper Large-scale all-optical electrophysiology links excitability and connectivity to circuit dynamics in vivo · claims file · checked 2026-10-21: ready
- jf608-brighter
In vivo, JF608-HTL is 3.6 times brighter than JF585-HTL with similar voltage sensitivity, giving a 50% increase in spike signal-to-noise ratio.
we found the redder JF608-HTL to be 3.6 times brighter, with similar voltage sensitivity, leading to a 50% increase in signal-to-noise ratio (SNR) in vivo
Results, Molecular and optical tools for wide-area all-optical electrophysiology, paragraph 1; Supplementary Figure 1A to EHow it will be judged
Same cells imaged with JF585-HTL, then with JF608-HTL ten days later, under the same 590 nm illumination (Supplementary Figure 1A to E). The paper does not say how the ratios are formed; readings (a) ratio of the mean over cells, (b) median of per-cell ratios. Reproduced when the ratio of photon counts and the SNR increase are within tolerance under one reading and both one-sided rank-sum tests give p <= 0.001.
- targeting-signal-to-background
Soma-targeted red illumination raised the signal-to-background ratio about 7.5-fold, from 0.15 +/- 0.05 to 1.12 +/- 0.32 (mean +/- s.d., 320 cells).
This targeting increased the signal-to-background ratio ∼7.5-fold, from 0.15 ± 0.05 to 1.12 ± 0.32 (mean ± s.d., n = 320 cells
Results, Molecular and optical tools, paragraph 4; Figure 1B, 1C; Supplementary Figure 5How it will be judged
Needs wide-field and targeted images of the same field. The paper does not define signal-to-background; readings (a) (cell fluorescence minus background) divided by background, (b) cell fluorescence divided by background, with background taken from the pixels around each soma outside any cell. Reproduced when both values are within tolerance under one reading.
- spike-snr-and-detection-errors
Single-spike SNR (spike height over baseline shot noise) was 4.5 +/- 0.7; the estimated false-discovery proportion of spike detection was 17 +/- 13% and the false-negative rate 28 +/- 19%.
The single-spike SNR (spike-height:baseline shot noise) was 4.5 ± 0.7 (mean ± s.d.). Using a fitted mixture model, we estimated the spike-detection false-discovery proportion to be 17 ± 13% across all neurons, and false-negative rate to be 28 ± 19%
Results, Molecular and optical tools, paragraph 5; Supplementary Figure 7How it will be judged
As in Methods, Detecting spikes; SNR is spike height (mean of the spike Gaussian of the two truncated Gaussian mixture) over shot noise (1.4826 times the median absolute deviation of the one-frame difference); error rates from the fitted mixture. Over the 520 cells of Supplementary Figure 7 (two mice). Which session and which 520 cells are not given; readings (a) the behavior sessions, (b) every session, with QC cells or all cells with a fit. Reproduced when the three means are within tolerance under one reading.
- snr-decay-one-hour
After 1 h of continuous imaging at 16 mW/mm2, spike SNR fell to 76 +/- 13% of its initial value.
After 1 h of continuous voltage imaging at 16 mW/mm 2 , the spike SNR decreased to 76 ± 13% of its initial value
Results, Molecular and optical tools, paragraph 5; Supplementary Figure 8How it will be judged
SNR per cell in 3 min chunks (Supplementary Figure 8A), n = 520 cells, two mice; the ratio of the chunk ending at 60 min to the first chunk, mean over cells. Whether the mean of ratios or ratio of means is meant is open; both are shown, and the claim holds when either is within tolerance.
- fig1d-stimulation-fold-change
Targeted stimulation of 76 randomly chosen cells raised their mean firing rate 16-fold, while the unstimulated cells rose only 1.4-fold.
Stimulation increased the average firing rate of the stimulated cells (blue) 16-fold, and of the un-stimulated cells (red) 1.4-fold
Figure 1D legend; Results, Molecular and optical tools, paragraph 6How it will be judged
From the 3 s stimulation epochs repeated every 40 s (Figure 1D); rate during stimulation epochs over rate outside them. Readings (a) ratio of population mean rates, (b) mean of per-cell ratios. The dandiset description does not list this session; if it is absent the claim cannot be tested.
- off-target-length-constants
Displacing the stimulation spot from the soma showed that off-target excitation decays with length constants of 47 um for subthreshold voltage and 25 um for firing rate.
we laterally displaced the stimulation spots from the somas and found the excitatory response decayed with length constants of 47 and 25 μm for subthreshold voltage and firing rate, respectively
Results, Molecular and optical tools, paragraph 6; Supplementary Figure 9How it will be judged
Lattice experiment of Methods, Characterization of blue light off-target effects (1000 trials, 20 distance bins of 15 um; voltage increase 60 to 190 ms after onset minus -130 to 0 ms; rate increase 0 to 130 ms minus -130 to 0 ms). The fit is not given; readings (a) exponential with no offset fitted to the population-average increase by bin, (b) the same on log values. The dandiset description does not list this session.
- l1-sampling-density
The recordings sampled about 20% of neurons in the focal plane and about 12% (320 of 2,702) of NDNF-positive L1 interneurons in the cylinder under the field of view; their density was 2,860 per mm3.
we recorded from ∼20% of the neurons in a focal plane of depth 50 μm and thickness ∼40 μm, and ∼12% (320/2,702) of all the NDNF-positive L1 interneurons
Results, Molecular and optical tools, paragraph 4; Supplementary Figure 6How it will be judged
Needs the spinning-disk z-stack (Supplementary Figure 6), segmented with a fine-tuned Cellpose 3.0 model; the dandiset description does not list it. If absent, the claim cannot be tested.
- adaptation-vadp-correlation
Spike-rate adaptation is weakly positively correlated with spike after-depolarization (R = 0.23, p = 1.9E-8, 564 neurons, 2 mice).
firing rate adaptation was positively correlated with spike after-depolarization (V adp; Supplementary Fig. 10E, R = 0.23, p = 1.9E-8, Pearson correlation, n = 564 neurons, 2 mice
Results, Intrinsic excitability, paragraph 3; Supplementary Figure 10EHow it will be judged
Per-cell adaptation (third step) and V_adp as defined in Methods, Calculating neural intrinsic excitability properties, from the sparseOpto sessions of both mice, pooled. The cells giving n = 564 are not stated; readings (a) QC cells with finite values of both properties, (b) all cells with finite values. Reproduced when R is within tolerance with p < 0.05 under one reading.
- fig2c-three-bins
Ward hierarchical clustering of the five z-scored intrinsic properties of the 320 cells of one mouse gives three bins of 94, 116 and 110 cells.
We divided these cells into 3 bins via hierarchical clustering (left panel), n = 94, 116, and 110 for clusters 1, 2, and 3 respectively
Figure 2C legendHow it will be judged
As in code, reproduce_figure2_from_nwb.m (linkage of the column-wise z-scored five properties of all 320 cells of M-YQ0201-29, Ward's method, cluster with maxclust 3), which the code README says should give these counts exactly; hence tolerance 0. The three counts are compared as a set, as cluster labels are arbitrary.
- fig2gk-bin-profiles
Bin 1 has the highest firing rate and the highest optical rheobase; bin 2 the lowest firing rate, the lowest adaptation and the highest membrane time constant; bin 3 the highest after-depolarization and adaptation and the lowest optical rheobase.
Bin 1 had both the highest firing rate and the highest optical rheobase (i.e. it required the greatest depolarization to begin spiking); bin 2 had the lowest firing rate and lowest spike-rate adaptation, and the highest membrane time constant; bin 3 showed the highest after-depolarization and spike-rate adaptation and the lowest optical rheobase
Results, Intrinsic excitability, paragraph 4; Figure 2G to KHow it will be judged
The paper calls these comparisons descriptive. Bins identified by their sizes (94, 116, 110). For each property the bin medians (the boxes of Figure 2G to K), after removing values more than 6 s.d. from the mean as the code does (rmoutliers, 'mean', ThresholdFactor 6). "Firing rate" is not named; readings (a) maximum firing rate (Figure 2I, one of the five properties), (b) the cluster-average firing rate of Figure 2F. Reproduced when all eight orderings hold; partially reproduced when six or seven hold. The code's two-sided rank-sum p values between bins are reported.
- two-mice-intrinsic-distributions
The two mice show similar broad distributions of intrinsic properties; by two-sided rank-sum tests they differ in optical rheobase (p <= 0.001) and membrane time constant (0.01 < p <= 0.05), not in V_adp, maximum rate or adaptation.
We repeated this protocol on two mice and saw similar broad distributions of intrinsic properties in both animals
Results, Intrinsic excitability, paragraph 3; Supplementary Figure 10H (marks read from the rendered PDF page 16)How it will be judged
Per property, two-sided rank-sum test between the sparseOpto sessions of the two mice. The legend gives n = 320 per mouse; readings (a) all cells with a finite value, (b) QC cells. Reproduced when rheobase and membrane time constant differ at p <= 0.05 and the other three do not; partially reproduced when four of the five calls match.
- synaptic-connection-counts
Optogenetic mapping found 802 inhibitory connections among 7,280 tested pairs in one mouse and 667 among 7,032 in the other, about 3 +/- 3 outgoing and 3 +/- 3 incoming per cell of 25 +/- 9 tested, a pairwise probability of 11 +/- 9% within 400 um.
We identified 802 statistically significant synaptic connections out of 7,280 pairs tested in one mouse, and 667 of 7,032 pairs tested in a second mouse. This corresponds to 3 ± 3 outgoing connections per cell and 3 ± 3 incoming connections per cell out of 25 ± 9 possible connections tested in each direction (mean ± s.d., n = 576 cells, 2 mice
Results, Synaptic inhibition, paragraph 6How it will be judged
Count of stored synaptic_connection flags among ordered pairs of QC cells at most 400 um apart, per mouse; the 60 to 400 um band is a second reading (code, loadFigure5SessionFromNWB.m lines 15 to 23, 800 connections for M-YQ0201-27 in the band, 814 without it, 667 for M-YQ0201-29). The paper's "pairs tested" may be (a) ordered pairs of QC cells within 400 um, or (b) pairs with a stored IPSP measurement; both shown. Per-cell probability is connections over pairs tested for that cell (outgoing), mean +/- s.d. over 576 cells.
- ipsp-median-amplitude
The median unitary IPSP among connected pairs was -2.8% of a spike height per presynaptic spike, while correlated spontaneous fluctuations were about 20% of a spike height.
Median unitary IPSP amplitude among connected cells was -2.8% of a spike height ... In contrast, correlated fluctuations were ∼20% of a spike height
Results, Synaptic inhibition, paragraphs 4 and 5How it will be judged
IPSP amplitude is the stored ipsp_amplitude_norm_per_presynaptic_spike (positive values, sign flipped), median over pairs with synaptic_connection set, both mice pooled; the per-mouse medians are shown. For the fluctuations the paper gives no method and no code computes the 20%; the reading chosen here is the code's cross-STA depolarization (code, reproduce_figure4_from_nwb.m, range of the quiet-state spike-triggered voltage over lags -100 to -2 frames, mean over pairs 60 to 400 um apart), per mouse and averaged. Reproduced when both are within tolerance (for the pooled or a per-mouse median).
- detection-limits
The mapping detected IPSPs with 50% probability at an amplitude of -2 +/- 1.1% of a spike, and spikelets at 0.8 +/- 0.48% of a spike.
This procedure established a 50% detection probability for IPSP amplitude of -2 ± 1.1% of a spike (mean ± s.d., n = 100 neuron-pairs from each mouse, near detection cutoff) ... This procedure established a 50% detection probability for spikelet amplitudes of 0.8 ± 0.48% of a spike
Results, Synaptic inhibition, paragraph 5; Results, Gap junction coupling, paragraph 3; Supplementary Figure 15How it will be judged
The paper and code do not say how the 50% point was estimated beyond "n = 100 neuron-pairs from each mouse, near detection cutoff". Readings (a) for the 100 pairs per mouse whose statistic lies nearest the Benjamini-Hochberg cutoff, the amplitude of each, mean +/- s.d.; (b) for those pairs, the amplitude of a scaled template added to null waveforms that is detected in half of the null draws. Reproduced when the mean is within tolerance under one reading.
- gap-junction-connection-counts
Spikelet mapping found 3,553 directed electrical connections among 7,280 tested pairs in one mouse and 2,199 among 7,032 in the other, 10 +/- 6 outgoing and 10 +/- 5 incoming per cell, a pairwise probability of 41 +/- 15%; the median spikelet was 1.2% of a spike.
We identified 3,553 statistically significant directed functional electrical connections out of 7,280 pairs tested in one mouse, and 2,199 of 7,032 in a second mouse. This corresponds to 10 ± 6 outgoing connections per cell and 10 ± 5 incoming connections per cell ... the pair-wise probability of unidirectional gap junction connections above our detection threshold was 41 ± 15%
Results, Gap junction coupling, paragraphs 2 and 3How it will be judged
As for synaptic-connection-counts, with the stored gap_junction_connection flag and spikelet_amplitude (frames 0 and 1 against frames -4, -3, -2, 4, 5, 6 of the cross-STA, Methods). The connection counts are taken in the 60 to 400 um band, as the code settles (loadFigure5SessionFromNWB.m lines 15 to 23 give 3553 for M-YQ0201-27 and 2199 for M-YQ0201-29 in that band); all pairs within 400 um is a variant. For "pairs tested" the readings of synaptic-connection-counts apply, with or without pairs under 60 um.
- hadamard-stimulation-rates
During Hadamard-coded stimulation, stimulated cells fired at 25.4 +/- 16.6 Hz and non-stimulated cells at 3.9 +/- 4.5 Hz; each cell received about 640 stimuli and fired about 12,380 evoked spikes in total.
Stimulated cells spiked rapidly (25.4 ± 16.6 Hz, mean ± s.d.) compared to non-stimulated cells (3.9 ± 4.5 Hz), and evoked spikes were largely uncorrelated between cells. Each cell received on average 640 stimuli, which elicited on average a cumulative 12,380 spikes per cell
Results, Gap junction coupling, paragraph 1How it will be judged
In the Hadamard chunks of the sparsePulseHad sessions, each QC cell's spike rate during its 750 ms on blocks and during its off blocks; mean +/- s.d. over cells, both mice pooled. Whether "non-stimulated cells" means cells in their off blocks or cells never stimulated in a block is open; the first is the reading, as every cell is stimulated with a 50% duty cycle.
- spikelet-not-scatter
Fluorescence scattered from a spiking cell decays over a much shorter distance than the spikelet amplitude (spikelet to scatter ratio above 2.5 at 60 um), so pairs under 60 um were excluded.
This scattered fluorescence signal decayed over a substantially shorter distance than the spikelet amplitude (at 60 μm separation, spikelet:scattered fluorescence > 2.5
Results, Gap junction coupling, paragraph 4; Supplementary Figure 17How it will be judged
Needs interstitial pixels within 400 um of each triggering cell (Methods), which only a movie holds; the dandiset has the raw movie for four blocks of one spontaneous session. Scatter STA normalized by the trigger cell's spike fluorescence (frame 0 minus frame -2), scatter spikelet extracted as a spikelet; 40 um distance bins (Supplementary Figure 17B). Reproduced when the ratio of mean spikelet to mean scatter in the bin at 60 um exceeds 2.25 and the scatter falls with distance faster than the spikelet.
- highmag-footprint
Under high-magnification imaging, spikelet amplitude was strongly correlated with the weight of the post-junctional cell's own spike footprint in the cross-STA image (R = 0.94, 720 pairs from 48 cells), supporting a somatic post-junctional origin.
Spikelet amplitude was strongly correlated with the coefficient of the self-STA footprint fitted to the cross-STA image (R = 0.94, p < 1E-15, n = 720 pairs from 48 cells
Results, Gap junction coupling, paragraph 5; Supplementary Figure 18DHow it will be judged
Needs the 7.5x high-magnification recordings (16 cells per field, Voltron2), which the dandiset description does not list. If present, the method of Methods, High magnification spikelet footprint analysis.
- lasso-off-target-correction
Correcting the IPSP matrix for spikes evoked in non-targeted cells by lasso regression changes little; the corrected and raw matrices correlate with R = 0.82 and fewer than 20% of significant IPSPs differ by more than 20%.
The two matrices are highly correlated, with a Pearson correlation coefficient of 0.82, p < 2E-308, n = 1755 pairs from 2 mice, and less than 20% of statistically significant IPSPs differ from the connectivity matrix by more than 20%
Methods, Analysis for mapping synaptic connections, paragraph 3; Supplementary Figure 16CHow it will be judged
Model IPSP matrix R = S W with S the evoked spikes per stimulus in targeted and non-targeted cells; W by lasso. The penalty and the choice of the 1755 pairs are not given; readings for the penalty (a) the value minimizing 10-fold cross-validated error, (b) the largest within one standard error of it. Reproduced when R is within tolerance and the fraction is below 22% under one reading.
- connection-distance-structure
Synaptic connectivity had an exponential degree distribution, a connection probability of 24% for cells under 150 um apart and a length constant of about 105 um; gap junction probability was 83% under 150 um with a 159 um length constant.
The synaptic connectivity matrix had a single-scale network structure 47 , with an exponential degree distribution. The probability of connection was 24% for closely separated cells (< 150 μm) and fell with a ∼105 μm length constant (Supplementary Fig. 19C,D). The gap junction matrix showed greater connectivity (connection probability 83% for cells separated by < 150 μm) and fell with a 159 μm length constant
Results, The structure of connectivity in L1, paragraph 1; Supplementary Figure 19C to FHow it will be judged
No code computes these. Probability is connected over tested ordered pairs of QC cells by distance, both mice pooled (per-mouse values shown). The fit is not given; readings (a) p(r) = A exp(-r/lambda) by least squares on binned probability, (b) a line fitted to log probability, with bins of 30 um (as Figure 3F, 3H) or 60 um (as Figure 3E, 3G), from 60 um (gap) or 0 um (synaptic) to 400 um. Degree distribution exponential when an exponential fits the in- and out-degree histograms better than a power law (lower residual on log counts), a reading chosen here. Reproduced when the four numbers are within tolerance under one reading and the degree distributions are exponential.
- fig3eg-amplitude-falls-with-distance
IPSP and spikelet amplitudes both decay with the distance between the cells.
IPSP and spikelet amplitudes both decayed with cell-cell distance
Figure 3E, 3G; Results, The structure of connectivity in L1, paragraph 2How it will be judged
As in code, reproduce_figure3_from_nwb.m panels E and G. IPSP pairs with stored amplitude above 1e-3 (no significance gate), spikelet pairs all, 60 to 400 um, six equal bins (linspace(60,400,7)), per mouse. The caption's 60 um bins give the same range. The connected-only selection is shown as a variant. Reproduced when, in both mice, the median in the nearest bin exceeds the median in the farthest bin for both measures and the Spearman correlation of amplitude with distance is negative at p < 0.05 (the test is a reading chosen here).
- fig3h-conduction-speed
Spikelet peak times increase with distance, giving a conduction speed of 0.28 m/s, consistent across two mice.
The spikelet peak times, determined by sub-frame interpolation, showed a distance-dependent time delay corresponding to a conduction speed of 0.28 m/s, consistent across n = 2 mice
Figure 3H; Results, The structure of connectivity in L1, paragraph 2How it will be judged
As in code, reproduce_figure3_from_nwb.m panel H. Mean Hadamard cross-spike STA of all pairs in twelve 30 um bins from 60 to 420 um (the caption's ten 30 um bins are the variant), each bin's time mean subtracted; coarse peak within 16 frames of lag 0; cubic fit over frames -2 to +4 around it and its maximum; delay in seconds at 1.27 ms per frame; distance regressed on delay with intercept, pooling 12 bins times 2 mice. Reproduced when the pooled speed is within tolerance; per-mouse speeds are shown.
- amplitudes-log-normal
IPSP and spikelet amplitudes both follow approximately log-normal distributions.
IPSP and spikelet amplitudes both followed approximately log-normal distributions
Results, The structure of connectivity in L1, paragraph 2; Supplementary Figure 19A, BHow it will be judged
Amplitudes of connected pairs, both mice pooled. The paper shows a Gaussian fit to the log histogram and no test. Reading chosen here, reproduced when, for both measures, the skewness of log amplitudes lies within -0.5 to 0.5 and the skewness of raw amplitudes exceeds 1.
- interaction-kernel
The population-average effect of one L1 spike is a brief excitatory pulse of about 2 ms spreading at 0.28 m/s with a decay length of about 160 um, followed by inhibition that peaks around 30 ms and decays with a time constant of about 35 ms.
a single L1 action potential evoked a brief excitatory pulse with a duration of ∼2 ms that rapidly propagated outward (0.28 m/s) with a ∼160 μm decay length constant, followed by a slower field of inhibition that peaked around 30 ms and decayed with a time constant of ∼35 ms
Results, The structure of connectivity in L1, paragraph 3; Supplementary Movie 3How it will be judged
The paper gives no method for Movie 3. The inhibitory part is read from the population-average IPSP waveform per presynaptic spike (blue_pulse_ipsp minus crosstalk, unconnected pairs counted as zero, as code panel 3F), the excitatory part from the population-average spikelet waveform (code panel 3H). Peak time measured from the stimulus or spike; decay from an exponential fitted after the peak; duration as full width at half maximum; length constant as in connection-distance-structure for the product of connection probability and mean amplitude. Readings for the time zero of the IPSP (a) pulse onset, (b) pulse end. Reproduced when the four values are within tolerance under one reading.
- fig3jk-presynaptic-sets-amplitude
IPSP amplitude of a pair is strongly correlated with the presynaptic cell's mean output to other cells (R = 0.61) and only weakly with the postsynaptic cell's mean input from other cells (R = 0.26).
The per-cell mean outgoing connection strength was a better predictor of single-synapse strength than was mean incoming connection strength (outgoing: R = 0.61, p = 1.1E-51, n = 497 pairs, vs. incoming: R = 0.26, p = 4.3E-9, n = 482 pairs
Figure 3J, 3K; Results, The structure of connectivity in L1, paragraph 4How it will be judged
As in code, reproduce_figure3_from_nwb.m (M-YQ0201-29). Pairs with synaptic_connection set, 60 to 400 um, IPSP tau SE/tau below its 90th percentile over all pairs with a defined SE, tau inside the range of positive tau values shrunk by 1e-3 at each end (code, tauLimits); leave-one-out arithmetic mean of the other pairs' amplitudes of the same presynaptic (J) or postsynaptic (K) cell; Pearson R on natural logs of pairs with both values positive. The code README expects R = 0.61 and 0.26 with a mask count of 561; the paper's n (497, 482) is read as the plotted pairs with a finite leave-one-out mean, shown with the counts. Reproduced when both R are within tolerance and the outgoing R exceeds the incoming R.
- fig3mn-postsynaptic-sets-decay
IPSP decay time constant is correlated with the mean time constant of other inputs to the postsynaptic cell (R = 0.33) and not with that of the presynaptic cell's other outputs (R = 0.07, p = 0.06).
The per-cell mean inbound synaptic time constant, 〈 τ kj 〉 k ≠ i , was a better predictor of single-synapse time constant τ ij than was mean outgoing time constant, 〈 τ ik 〉 k ≠ i (incoming: R = 0.33, p = 4.7E-18, n = 651 pairs, vs. outgoing: R = 0.07, p = 0.06 , n = 653 pairs
Figure 3M, 3N; Results, The structure of connectivity in L1, paragraph 5How it will be judged
As fig3jk-presynaptic-sets-amplitude, on ipsp_decay of M-YQ0201-27 (code; README expects R = 0.07 and 0.33, mask count 706). Reproduced when the incoming R is within tolerance with p < 0.05 and the outgoing correlation is not significant (p >= 0.05, the paper's test for its absence); the outgoing R and p are reported either way.
- fig3lo-variance-components
A linear mixed-effects model attributes more variance of IPSP amplitude to presynaptic than to postsynaptic identity, and more variance of IPSP decay time constant to postsynaptic than to presynaptic identity, each ordering holding in all but under 0.1% of bootstrap simulations.
More variance of IPSP amplitude is explained by presynaptic identity than by postsynaptic identity ... ***: < 0.001 of the simulations produced higher postsynaptic variance ... More variance of IPSP decay time constant is explained by postsynaptic identity than by presynaptic identity
Figure 3L, 3O legends; Methods, Linear mixed effects modelHow it will be judged
As in code, tutorials/tutorial5_pre_post_variance. Connected QC pairs of both mice at 60 um or more, positive amplitude; log response ~ 1 + animal + distance term + (1|pre) + (1|post), distance term linear or log distance chosen by AIC of ML fits; decay weighted by 1/(SE^2 + s0^2); REML; 2000 parametric bootstrap refits (seeds 12012, 12014). Reproduced when presynaptic variance exceeds postsynaptic for amplitude and postsynaptic exceeds presynaptic for decay, each in more than 99.9% of the bootstrap replicates.
- gap-junction-no-identity-effect
Gap-junction strength shows little association with pre- or post-junctional identity.
The gap junction connection strength showed little association with pre- or post-junctional identity in this analysis
Results, The structure of connectivity in L1, paragraph 5How it will be judged
The analysis of fig3jk-presynaptic-sets-amplitude applied to spikelet_amplitude of pairs with gap_junction_connection set, 60 to 400 um, each mouse. No number is given; reading chosen here, reproduced when both the outgoing and the incoming log-scale Pearson R are below 0.26, the value the paper calls a weak correlation, in both mice.
- subthreshold-correlation-length
In the quiet state subthreshold voltages of nearby cells (60 to 120 um) correlate at 0.6 and the correlation decays with a 2.4 mm length constant; in the whisking state the values are 0.5 and 4.0 mm.
In the quiet state, the voltage dynamics were strongly correlated between nearby cells (correlation = 0.6, 60 μm < r < 120 μm) and decayed with an exponential length constant of 2.4 mm ( Fig. 4B ; Supplementary Fig. 20D); in the whisking state, the short-range correlation was 0.5 and the decay length constant was 4.0 mm
Results, Spontaneous spikes and subthreshold voltages have distinct spatiotemporal dynamics, paragraph 3; Figure 4B; Supplementary Figure 20A, DHow it will be judged
As in code, reproduce_figure4_from_nwb.m STATS. Stored state-dependent voltage cross-correlations; 60 um distance bins from 60 to 1800 um; zero-lag value of the 60 to 120 um bin; length constant 1/slope of a line fitted to log zero-lag correlation against distance over all non-empty bins; per mouse, then averaged over the two mice. Recomputing the cross-correlation from the voltage (normalized by the lag-1 s.d.) is a variant. Reproduced when the four values are within tolerance.
- subthreshold-low-dimensional
Subthreshold dynamics are low dimensional; the first 10 principal components explain 72% of the variance in the quiet state and 62% in the whisking state.
principal components analysis (PCA) showed that the first 10 components accounted for 72% of the variance in the quiet state and 62% of the variance in the whisking state
Results, Spontaneous spikes and subthreshold voltages, paragraph 3; Supplementary Figure 21BHow it will be judged
As in Methods, Dimensionality of subthreshold fluctuations; covariance of the subthreshold voltage of the behavior session per state, diagonal replaced by the lag-1 variance where the voltage is not smoothed, eigenvalues over total variance. No code. Open, with readings (a) the stored subthreshold voltage (smoothed, diagonal kept), (b) the normalized voltage with the lag-1 diagonal; and per mouse or averaged over the two mice. Reproduced when both values are within tolerance under one reading, with the quiet value above the whisking value.
- quiet-state-oscillations
In the quiet state, but not the whisking state, subthreshold dynamics often show global oscillations between 1 and 10 Hz.
In the quiet state - but not the whisking state - the subthreshold dynamics often showed global oscillations between 1 and 10 Hz
Results, Spontaneous spikes and subthreshold voltages, paragraph 4; Supplementary Figure 21A, CHow it will be judged
Population-average Welch power spectrum of the subthreshold voltage per state (Methods, Frequency spectrum; Welch segment length a standard choice, 2 s). Reading chosen here, reproduced when in both mice the power integrated over 1 to 10 Hz is higher in the quiet than in the whisking state.
- traveling-waves
Quiet-state oscillations are traveling waves with various directions, a slight bias toward medial-posterior, and a mean speed of 18.2 +/- 8.3 mm/s (3,858 events, 2 mice); a 5 Hz oscillation has a wavelength of about 4 mm.
with a slight bias toward the medial-posterior direction and an average speed of 18.2 ± 8.3 mm/s (mean ± s.d., n = 3858 events, 2 mice). For a typical 5 Hz oscillation, the wavelength was ∼4 mm
Results, Spontaneous spikes and subthreshold voltages, paragraph 4; Supplementary Figure 21D to HHow it will be judged
As in Methods, Wave propagation analysis. Events are peaks of the derivative of the population-average voltage above 3.5 times its s.d. during whisking, in quiet epochs; each event spans the voltage minimum to maximum flanking the peak; speed is the slope of pairwise distance against lag of peak cross-correlation. No code. The slope can be read (a) as distance regressed on lag, (b) lag regressed on distance and inverted; both shown. Direction from the phase gradient (Hilbert phase, 325 um Gaussian smoothing, 160 um grid). Reproduced when the mean speed and the event count are within tolerance under one reading and the circular mean direction lies in the medial-posterior quadrant.
- spike-synchrony-localized
Spike-rate cross-correlograms peak sharply in space (length constants of 277 um quiet and 270 um whisking) and time (50% decay by 2.5 ms lag), unlike subthreshold correlations (2.4 mm, full width at half maximum 80 ms).
While the subthreshold cross-correlations decayed slowly over space (quiet-state length constant 2.4 mm) and time (quiet-state full-width at half-maximum 80 ms), the spike-rate cross-correlogram had a peak that was sharply localized in space (length constants of 277 and 270 μm for quiet and whisking state respectively) and time (decayed by 50% at lags of just 2.5 ms
Results, Spontaneous spikes and subthreshold voltages, paragraph 5; Figure 4C, 4D; Supplementary Figure 20F, GHow it will be judged
As in code, reproduce_figure4_from_nwb.m STATS. Synchrony is the correlogram maximum over lags -1 to 1 frame minus the larger of the means over frames -5 to -3 and 3 to 5 (Supplementary Figure 20G); length constants by log-linear fit per mouse, averaged. Readings for the 277 and 270 um (a) the synchrony fit restricted to r < 800 um, (b) the fit of the 2.5 ms-lag correlogram over all bins. FWHM is the code's quiet-state median over bins. The 2.5 ms is read as the half-width of the correlogram peak in the 60 to 120 um bin (code spikeHalfWidth, whisking state as in the code; quiet as a variant). Reproduced when all four values are within tolerance under one reading.
- voltage-to-spike-sigmoid
Each cell's spontaneous voltage-to-spike relationship (conditional spike rate as a function of subthreshold voltage) is sigmoidal, with substantial cell-to-cell variation in threshold and maximum rate.
These curves all had a characteristic sigmoidal shape, with substantial cell-to-cell variations in threshold and maximum firing rate
Results, Threshold nonlinearities and private excursions, paragraph 2; Figure 4E, 4FHow it will be judged
Quiet-state frames without running; P(spk|V) as the histogram of V at spike times over the histogram of all V, divided by 1.27 ms; voltage bins of 0.04 SH from -2 to 2 (code, reproduce_figure4_from_nwb.m). The Methods/caption say V in the 10 ms before spikes, the code uses the sample at the spike frame (the code notes the author kept the wording); both shown. Reading chosen here, reproduced when for more than half of cells a four-parameter logistic fitted over bins holding at least 100 frames explains at least 90% of the variance, and the fitted midpoints and maxima have coefficients of variation above 0.2 across cells.
- fig4g-private-depolarizations
Voltages of neighbouring cells (under 200 um) are most correlated near rest and during hyperpolarizing fluctuations, and much less as voltage approaches spike threshold.
The correlation between V i and V j was strongest near resting potential and for hyperpolarizing fluctuations, but was markedly reduced as the subthreshold voltage approached spike threshold
Results, Threshold nonlinearities and private excursions, paragraph 3; Figure 4GHow it will be judged
As in code, reproduce_figure4_from_nwb.m panel G. Pairs 60 to 200 um apart, both orderings, quiet frames without running, 100 voltage bins from -2 to 2 SH, counts pooled over both mice, P(V_j|V_i). Reading chosen here, reproduced when the slope of the conditional mean of V_j on V_i over V_i from -0.5 to 0.2 SH is at least twice the slope over V_i from 0.5 to 1 SH.
- fig4hi-self-sta-diverges
For cells under 200 um apart, self- and cross-STAs of membrane voltage track each other at lags beyond 30 ms, but the spiking cell has a higher baseline and an upward divergence in the 30 ms before its spike.
For cells separated by < 200 μm, the subthreshold components of these two waveforms closely followed each other at lags > 30 ms ( Fig. 4H ). However, the spiking cell saw both a higher baseline and an upward divergence in the self-STA in the 30 ms preceding the spike
Results, Threshold nonlinearities and private excursions, paragraph 4; Figure 4H, 4IHow it will be judged
Stored quiet-state spike-triggered voltage, pairs 60 to 200 um (Results, "< 200 um", with the 60 um scatter cut of Figure 4B; code panel H draws its examples from this band, panel I uses all distance bins), per mouse. Reading chosen here, reproduced when in both mice the mean self-STA minus the mean cross-STA is larger at -5 ms than at -30 ms by more than the s.d. of that difference over lags -140 to -30 ms, and the self-STA is above the cross-STA at -30 ms.
- fig5a-rheobase-predicts-spontaneous-excitability
Cells with higher optical rheobase fire less at a given subthreshold voltage, both under ramp stimulation and during quiet spontaneous activity.
in both datasets, cells with higher optical rheobase showed lower firing rate for a given subthreshold depolarization
Figure 5A; Results, Intrinsic properties shape subthreshold-to-spiking transfer functions, paragraph 1How it will be judged
As in code, reproduce_figure5_from_nwb.m panel A (M-YQ0201-27, n = 280 cells). Bins by rheobase, five equal-width bins between its 1st and 99th percentiles (code; the caption's quintiles as a variant); P(spk|V) pooled counts per bin, V bins of 0.05 SH; spontaneous from quiet non-running chunks with no blue within 80 um; evoked from the first half of the ramp. Reproduced when, at V = 0.5 SH, rate falls across the five bins with Spearman rho below -0.8 in both conditions (a reading chosen here).
- supp22-rheobase-correlations
Optical rheobase is negatively correlated with the conditional spike rate at V = 0.5 SH, both evoked (R = -0.59) and spontaneous (R = -0.32).
Correlation between optogenetically evoked conditional spike rate at VV= 0.5 and optical rheobase. R = -0.59 (Pearson correlation), p = 7.8e-52, n = 543 ... Correlation between spontaneous activity conditional spike rate at VV= 0.5 and optogenetically measured rheobase. R = -0.32 (Pearson correlation), p = 4.1e-14, n = 543
Supplementary Figure 22A, BHow it will be judged
Per cell, P(spk|V) as in fig5a in the bin containing V = 0.5 SH, both mice pooled. No code. Which 543 cells is open (QC cells give 576); readings (a) QC cells with a finite rate at 0.5 SH in both conditions, (b) cells passing the 1st to 99th percentile rheobase range in each mouse. Reproduced when both R are within tolerance under one reading.
- fig5b-adaptation-dvdt
Cells with more spike-rate adaptation spike preferentially in response to rapidly rising subthreshold voltage during spontaneous activity (R = 0.26 between adaptation and the conditional rate at dV/dt = 0.35).
Cells with higher spike-rate adaptation preferentially spiked in response to rapidly rising inputs
Figure 5B; Results, Intrinsic properties shape subthreshold-to-spiking transfer functions, paragraph 2; Supplementary Figure 22CHow it will be judged
P(spk|dV/dt) in quiet spontaneous activity with V restricted to 0.2 to 0.8 SH (Methods). The Methods shift dV/dt by 6 ms; the code (panel B) uses an 8-frame centred difference shifted by 4 frames, a median-threshold quiet rule, and a V window applied to 0.25 SH bin centres, in effect 0.25 to 0.75 SH; both shown, Methods first. Per cell, the rate at dV/dt = 0.35, against adaptation, both mice, cells as in supp22-rheobase-correlations. Reproduced when R is within tolerance with p < 0.05 and, in the panel B quintile curves, the highest-adaptation bin has the highest rate at dV/dt = 0.35.
- fig5c-adp-bursting
Cells with greater after-depolarization fire more bursts during spontaneous activity (R = 0.52 between V_adp and the 2.5 to 15 ms autocorrelogram).
Cells with greater after-depolarization were more likely to fire spikes in bursts
Figure 5C; Results, Intrinsic properties shape subthreshold-to-spiking transfer functions, paragraph 3; Supplementary Figure 22DHow it will be judged
Burst rate is the mean spike autocorrelogram from lag 2.5 to 15 ms (Methods, Average firing rate and average burst rate), from spontaneous activity in quiet and whisking (Results), both mice, cells as in supp22-rheobase-correlations. The code (panel C) triggers on quiet-state spikes only; shown as a variant. Reproduced when R is within tolerance with p < 0.05.
- fig5e-inhibition-in-spontaneous-voltage
Relative to distance-matched unconnected controls, a presynaptic spike is followed 15 to 30 ms later by a postsynaptic hyperpolarization of -2.1% of a spike height for the strongest quintile of connections and -1% at median strength; unconnected control pairs instead rise by 1% of a spike height from -20 to -5 ms to 15 to 30 ms.
For cell-pairs in the top quintile of synaptic strength, a presynaptic spike induced a median postsynaptic voltage decrease of -2.1% of a spike height in the 15 - 30 ms after a spike, relative to the distance-matched unconnected controls (p = 1.9E-33, n = 293 cell pairs, 2 mice). For the median synaptic strength (among connected pairs), this hyperpolarization was -1% of a spike height (p = 5.7E-39, n = 1,467 cell pairs, 2 mice, Wilcoxon rank sum test ... The STA waveform showed an increase by 1% of a spike height in the interval 15 – 30 ms after the triggering spike vs. the -20 to - 5 ms before the spike
Results, Local connectivity shapes network dynamics, paragraph 2; Figure 5D, 5E; Supplementary Figure 23FHow it will be judged
Voltage suppression per pair is frames 12 to 25 minus frames -17 to -4 of the spontaneous cross-STA (Methods, Effect of connections). Connected pairs with synaptic_connection set, 60 to 400 um, quintiles of IPSP amplitude, both mice; controls per Methods (cell k within 400 um of i and j, not connected to i). No code for the numbers. Open, with readings (a) median over connected pairs of suppression minus the median over their controls; (b) median over connected pairs of (pair suppression minus mean over its own controls); (c) suppression of the quintile average after regressing out the control average (Methods, Estimating cross STAs). "Median strength" read as all connected pairs (n = 1,467) or as the third quintile; both shown. Test, rank-sum of pair suppressions, connected against controls, one-sided (Supplementary Figure 23F) and two-sided. Reproduced when both values are within tolerance under one reading and both tests give p < 0.05.
- fig5e-inhibition-in-spontaneous-rate
For the strongest quintile of synaptic connections, a presynaptic spike lowers the postsynaptic rate by 0.18 Hz 5 to 13 ms later, a loss of 7e-3 spikes over the IPSP; near median strength, by 0.083 Hz, a loss of 2.7e-3 spikes.
For cell-pairs in the top quintile of synaptic strength, a presynaptic spike induced a median postsynaptic decrease in spike rate of 0.18 Hz in the 5-13 ms after the triggering spike, measured relative to nearby non-connected controls. Integrating the decrease in spike rate over the entire IPSP duration gave a median loss of 7×10 -3 spikes in the post-synaptic cell. For cell-pairs near median synaptic strength (among connected pairs), this decrease was 0.083 Hz, corresponding to a loss of 2.7×10 -3 spikes
Results, Local connectivity shapes network dynamics, paragraph 3; Figure 5E; Supplementary Figure 23D, HHow it will be judged
Rate suppression is frames 4 to 10 minus frames -10 to -4 of the spontaneous cross-correlogram (Methods), in Hz; readings for the comparison with controls and for "median strength" as in fig5e-inhibition-in-spontaneous-voltage. The integration window for spikes lost ("the entire IPSP duration") is open; readings (a) 0 to 100 ms, (b) from 0 ms to where the control-subtracted rate returns to zero. Reproduced when the four values are within tolerance under one reading.
- fig5g-gap-junction-synchrony
Gap-junction coupling raises spontaneous spike synchrony; for the strongest quintile, synchronous firing (lag <= 2.5 ms) exceeds near-synchronous firing by 0.86 Hz more than in unconnected neighbours, and by 0.32 Hz at median coupling.
for cell-pairs in the top quintile of gap junction coupling, the rate of synchronous firing (time lag ≤ 2.5 ms) was 0.86 Hz greater than near-synchronous firing (time lag 5 ms, p = 8.6E-53, n = 1151 pairs, 2 mice, Wilcoxon rank sum test against unconnected neighbors; Supplementary Fig. 23I). Integrating the change in spike rate across the entire spikelet duration gave a gain of 1.7×10 -3 spikes. For the median gap-junctional coupling, the synchrony enhancement was 0.32 Hz (p = 1.9E-61, n = 5752 pairs, 2 mice, Wilcoxon rank sum test against unconnected neighbors), corresponding to a gain of 7×10 -4 spikes
Results, Local connectivity shapes network dynamics, paragraph 4; Figure 5F, 5G; Supplementary Figure 23IHow it will be judged
Synchrony per pair is the maximum of the cross-correlogram over frames -1 to 1 minus the mean of the 3 frames before frame -1 or after frame 1, whichever is larger (Methods). Pairs with gap_junction_connection set, 60 to 400 um; n = 5752 is 3553 + 2199, the counts the code gives in that band (loadFigure5SessionFromNWB.m lines 15 to 23), and Results, Gap junction coupling, paragraph 4, excludes pairs under 60 um from further analysis. Readings for the comparison with controls and for "median coupling" (all pairs or third quintile) as in fig5e-inhibition-in-spontaneous-voltage; spikes gained integrated over the spikelet duration, readings (a) frames -1 to 1, (b) lags with control-subtracted rate above zero around lag 0. Reproduced when the four values are within tolerance under one reading and both rank-sum tests give p < 0.05.
- inhibition-gap-balance
Scaled by connection probability, spikes lost to inhibition per connected pair (2.7e-3, about four times the 7e-4 gained by gap junctions) and spikes gained from gap junctions are approximately balanced.
Hence, oppositely acting synaptic and gap-junctional influences are approximately balanced
Results, Local connectivity shapes network dynamics, paragraph 5How it will be judged
Product of median spikes lost per synaptic pair and synaptic connection probability, against product of median spikes gained per gap-junction pair and gap junction probability, from the values of the claims it depends on (the paper's own numbers give 3.0e-4 and 2.9e-4). Reading chosen here, reproduced when the ratio of the two products lies between 0.5 and 2.
- npy-fraction-and-similarity
About 49% of recorded neurons are NPY-positive (166 of 320 and 145 of 320); the two subtypes are intermixed and have similar spike SNR and mean spike rate.
Approximately 49% of recorded neurons were NPY (+) (166/320 in mouse 1, 145/320 in mouse 2). The two subtypes were intermixed throughout the field of view, and had similar spike SNR and similar average spike-rate
Results, Brain state differentially modulates functional and genetic L1 interneuron subtypes, paragraph 1; Supplementary Figure 24A to DHow it will be judged
Stored gfp_positive over all 320 cells per mouse; which mouse is "mouse 1" is not stated, so the two counts are compared as a set. Similar SNR and rate (Supplementary Figure 24B, D, 257 NPY- and 248 NPY+ behavior-session cells), reading chosen here, two-sided rank-sum p >= 0.05 or a difference of medians under 10%. Intermixed, reading chosen here, a two-sided Kolmogorov-Smirnov test of x and y coordinates between subtypes with p >= 0.05 in each mouse. Reproduced when the counts are within tolerance and both similarity tests hold.
- npy-intrinsic-differences
NPY-negative neurons have greater after-depolarization, lower optical rheobase, more spike-rate adaptation, slightly lower maximum firing rate and a shorter membrane time constant than NPY-positive neurons, each difference at p <= 0.001.
The NPY (-) neurons had greater after-depolarization, lower optical rheobase, more spike-rate adaptation, slightly lower maximum firing rate, and a shorter membrane time constant
Results, Brain state differentially modulates functional and genetic L1 interneuron subtypes, paragraph 2; Figure 6B, 6C; Supplementary Figure 24E (marks read from the rendered PDF page 39)How it will be judged
Per-cell properties from the sparseOpto sessions of both mice, QC cells, grouped by gfp_positive; two-sided rank-sum test per property. The legend's n (257, 248) matches the behavior-session cells; readings (a) QC cells of the sparseOpto sessions, (b) cells on the behavior-session correlation index. Reproduced when all five differ in the stated direction at p <= 0.001 under one reading; partially reproduced when four do.
- npy-classifier
A logistic-regression classifier on the five intrinsic properties identifies NPY status with 78% cross-validated balanced accuracy (95% CI 74 to 81%) against 50% (46 to 55%) for shuffled labels; after-depolarization is the most informative feature.
Using these five electrophysiological parameters, a logistic-regression classifier identified cell type with 78% (95% CI [74%, 81%]) cross-validated balanced accuracy, compared with a 50% (95% CI [46%, 55%]) chance level. The most impactful feature for cell-type classification was spike afterdepolarization
Results, Brain state differentially modulates functional and genetic L1 interneuron subtypes, paragraph 2; Methods, Cell type classificationHow it will be judged
Tolerances from the confidence intervals (the wider side). Logistic regression on the five properties, trained on 80% and tested on 20% of cells, 10,000 resampled folds, 2.5 and 97.5 percentiles; control by 5-fold cross-validation with shuffled labels (Methods). No code. Open, with readings for the cells (a) QC cells of both sparseOpto sessions pooled, (b) each mouse; for scaling, (a) z-scored features, (b) raw; and for the most impactful feature, (a) largest absolute coefficient on z-scored features, (b) largest drop in balanced accuracy when the feature is left out. Reproduced when both values are within tolerance and V_adp is the top feature under one reading of each.
- npy-connection-probability
NPY-positive cells are more likely to synapse onto other L1 interneurons (outgoing probability within 400 um 14 +/- 15%) than NPY-negative cells (7 +/- 11%).
NPY (+) cells were significantly more likely to synapse onto other L1 interneurons of either class (outgoing connection probability within 400 μm: 14 ± 15%, n = 307 NPY (+) cells, 2 mice) compared to NPY (-) cells (connection probability: 7 ± 11%, n = 269 NPY (-) cells, 2 mice, P < 0.001, Wilcoxon rank sum test
Results, Brain state differentially modulates, paragraph 3; Figure 6D; Supplementary Figure 25AHow it will be judged
Per QC cell of the sparsePulseHad sessions (576 = 307 + 269), outgoing synaptic connections over tested partners within 400 um, grouped by gfp_positive; two-sided rank-sum. Reproduced when NPY+ exceeds NPY- with p < 0.001 and the means are within tolerance.
- npy-ipsp-amplitude
IPSPs from NPY-positive presynaptic cells are larger (-3.7 +/- 2.7% of a spike height, 977 pairs) than from NPY-negative cells (-3.1 +/- 2.3%, 490 pairs).
The IPSP amplitudes averaged across all detected synaptic connections were significantly larger for NPY (+) presynaptic cells (−3.7 ± 2.7% of a spike height, n = 977 pairs, 2 mice) than for NPY (-) presynaptic cells (−3.1 ± 2.3% of a spike height, n = 490 pairs, P < 0.001, Wilcoxon rank sum test
Results, Brain state differentially modulates, paragraph 3; Supplementary Figure 25BHow it will be judged
Stored IPSP amplitudes of pairs with synaptic_connection set, 60 to 400 um, both mice (1,467 pairs as in fig5e, 800 + 667 in that band by the code), grouped by presynaptic gfp_positive; two-sided rank-sum. Reproduced when NPY+ amplitudes are larger with p < 0.001 and the means are within tolerance.
- npy-ipsp-duration
IPSPs last longer in NPY-positive postsynaptic cells (58 +/- 63 ms, 699 pairs) than in NPY-negative cells (43 +/- 54 ms, 646 pairs).
For synaptic inputs, IPSP durations were significantly longer in NPY (+) postsynaptic cells (58 ± 63 ms, n = 699 pairs, 2 mice) than in NPY (-) cells (43 ± 54 ms, n = 646 pairs, 2 mice, P < 0.001
Results, Brain state differentially modulates, paragraph 3; Supplementary Figure 25CHow it will be judged
Duration is the IPSP decay time constant (Supplementary Figure 25C, whose group counts sum to 699 and 646), stored ipsp_decay of connected pairs with a finite fit, both mice, grouped by postsynaptic gfp_positive; two-sided rank-sum. Reproduced when NPY+ is longer with p < 0.001 and the means are within tolerance.
- npy-gap-junction-no-difference
Outgoing and incoming gap-junction connectivity does not differ systematically between NPY-positive and NPY-negative cells.
The gap junction out-going and incoming connectivity did not differ systematically between NPY (+) and NPY (-) sub-types
Results, Brain state differentially modulates, paragraph 3; Supplementary Figure 25D, E (marks read from the rendered PDF page 41)How it will be judged
A claim of absence, on the paper's test, two-sided rank-sum tests among the four pre/post subtype groups of per-cell gap-junction connection probability (Supplementary Figure 25D) and pair spikelet amplitude (25E). The published panels mark several pairwise differences as significant, so "systematically" is read as a consistent direction. Reproduced when there is no subtype effect significant at p <= 0.05 in the same direction in both matched comparisons, for outgoing ((-) to (-) against (+) to (-), and (-) to (+) against (+) to (+)) and for incoming ((-) to (-) against (-) to (+), and (+) to (-) against (+) to (+)); not reproduced otherwise. Effect sizes are given either way.
- npy-subthreshold-similar
Population-average subthreshold voltages of NPY-positive and NPY-negative cells are almost indistinguishable (R = 0.97, slope 0.96).
The population-average subthreshold voltages were almost indistinguishable between NPY (+) and NPY (-) subpopulations ( R = 0.97, slope = 0.96
Results, Brain state differentially modulates, paragraph 4; Figure 6E, 6HHow it will be judged
Tolerance on R set to 0.03, as R cannot exceed 1. Mean subthreshold voltage over NPY+ cells and over NPY- cells of the behavior session of M-YQ0201-29 (Figure 6H; 117 and 141 cells), frame by frame. No code. Open, with readings for the frames (a) all frames of the first 2000 s, (b) non-running frames; and for the slope (a) NPY+ regressed on NPY-, (b) the reverse. Reproduced when both values are within tolerance under one reading.
- npy-umap-groups
Clustering spontaneous firing patterns alone gives two groups that co-assort with NPY status; 157 of 203 group 1 cells are NPY-negative and 202 of 302 group 2 cells are NPY-positive.
The sorted spike raster clearly showed two subpopulations (Group 1 and 2, Fig. 6E,F ), which co-assorted with the NPY (-) and NPY (+) subtypes respectively (157/203 Group 1 cells were NPY (-) and 202/302 Group 2 cells were NPY (+) , n = 2 mice
Results, Brain state differentially modulates, paragraph 4; Figure 6E to GHow it will be judged
As in code, reproduce_figure6_from_nwb.m (E to G). Spike trains with frames where more than 15 cells spike zeroed, rates in 500 ms box bins over the first 2000 s, z-scored per cell, projected by svds (u*s) as the UMAP input, UMAP (n_neighbors 20, 2 components), k-means k = 2, each behavior session separately, groups labelled by matching group-mean to subtype-mean rates; the Methods' 500 ms moving average is a variant. UMAP and k-means are unseeded; run with 10 seeds and report the spread. Reproduced when the median counts over seeds are within tolerance and the association of group with NPY status has p < 0.05 by Fisher's exact test (a test chosen here).
- npy-whisking-onset-rates
At whisking onset NPY-positive cells raise their spike rate from 1.4 +/- 1.7 Hz to 2.8 +/- 4.3 Hz, while NPY-negative cells show no significant change (1.8 +/- 2.1 Hz to 2.0 +/- 2.6 Hz).
In NPY (+) cells, spike rate increased from 1.4 ± 1.7 Hz to 2.8 ± 4.3 Hz (n = 248 cells, N = 2 mice, P < 0.001, Wilcoxon rank sum test). In NPY (-) cells, spike rate did not show a significant change (from 1.8 ± 2.1 Hz to 2.0 ± 2.6 Hz, n = 257 cells, N = 2 mice
Results, Brain state differentially modulates, paragraph 4; Figure 6H, 6J; Supplementary Figure 26BHow it will be judged
Whisking onsets by the lasso deconvolution of Methods (lambda 1 to 15 chosen to minimize whisking variance in the 2 s before onset; the code uses the stored reconstructions and keeps onsets more than 1.5 s apart). Per cell, mean rate in the 640 ms before and after each onset, averaged over onsets (Supplementary Figure 26B), both behavior sessions (505 cells). Two-sided rank-sum test, before against after, per subtype, as the paper names it; the signed-rank test is a variant. Reproduced when NPY+ rises with p < 0.001 and NPY- shows no change at p > 0.05 (the absence judged on the rank-sum test).
- npy-oscillation-peak-rates
At the peaks of quiet-state subthreshold oscillations, NPY-negative cells spike at a higher rate than NPY-positive cells, while their mean subthreshold voltages do not differ.
NPY(-) cells spiked at a higher rate during quiet-state subthreshold oscillations
Supplementary Figure 26A; Figure 6IHow it will be judged
Peaks of the population-average subthreshold voltage band-passed 1.5 to 10 Hz above zero in quiet epochs (Methods, Oscillation peak detection; code, reproduce_figure6_from_nwb.m, butter(4, [1.5 10]*2/fs) with filtfilt). Per cell, the peak-triggered average voltage and rate (Supplementary Figure 26A). How a cell's value is taken from it is not stated; readings (a) the mean over the code's Figure 6I window of +/- 300 frames (+/- 381 ms), (b) the value at the peak frame. Both behavior sessions. Reproduced when the rate differs at p <= 0.001 with NPY- higher and the voltage does not differ at p <= 0.05.
- npy-state-dependent-excitability
Whisking decreases the excitability of NPY-negative cells and increases that of NPY-positive cells; in the quiet state NPY-negative cells spike faster at a given voltage, in the whisking state NPY-positive cells do.
Whisking induced a significant decrease in NPY (-) excitability and a significant increase in NPY (+) excitability ... In the quiet state the NPY(-) cells spiked faster and in the whisking state the NPY(+) cells spiked faster
Results, Brain state differentially modulates, paragraph 5; Figure 6K; Supplementary Figure 26C (marks read from the rendered PDF page 43)How it will be judged
Per cell, P(spk|V) for V between 0.4 and 0.6 SH (Supplementary Figure 26C), in quiet epochs and in the 640 ms after whisking onsets without running (code uses frames 0 to 500 after onset, 635 ms), both behavior sessions. Two-sided rank-sum tests. Reproduced when the four comparisons (NPY- quiet above whisking, NPY+ whisking above quiet, NPY- above NPY+ in quiet, NPY+ above NPY- in whisking) each hold with p <= 0.05; partially reproduced when the two within-subtype comparisons hold.
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