Probing subthreshold dynamics of hippocampal neurons by pulsed optogenetics (DANDI:000568)

Claims

From the paper Probing subthreshold dynamics of hippocampal neurons by pulsed optogenetics

Reproducing Valero et al. (2022) from dandiset 000568 16

Notebook reproduce_valero_2022.ipynb

Not reproducedMain text, paragraph 4; Figure 2, A and B
During track running, the light-induced rate gain is largest at the trough of the theta cycle (P < 1e-6, Wilcoxon test).
We observed a gain at the trough of the theta cycle, the phase corresponding to the strongest synchrony of pyramidal neurons (Fig. 2A)
Main text, paragraph 4; Figure 2, A and B
What the paper reports
- Wilcoxon test, p < 10⁻⁶
In 57 light-responsive putative pyramidal cells during laps, the gain is 2.04 Hz in the trough half of theta and 2.07 Hz in the peak half (medians), higher at the trough in 22 of 57 cells (Wilcoxon p = 0.14) and significant in neither session. In 60-degree bins the gain is largest 30 degrees after the peak (2.13 Hz). The stored LFP rate is 1250 Hz from 0 s and the LFP ends with the last epoch; ripple-band power at 44 and 27 deposited ripple peaks inside the Maze epoch is 113 and 78 times its mean; spikes of putative pyramidal cells in control windows have a circular mean phase of 128 and 130 degrees, in the trough half; the theta-band LFP averaged around onsets deviates by at most 27.1 and 8.5 against a theta-band SD of 406 and 770.
How the test differed from the paper’s method
- Two sessions of one mouse.
- The LFP channel (largest ripple power), the theta band (6 to 10 Hz) and the half-cycle split are choices made here; the paper's are in its unavailable Methods.
Not reproducedMain text, paragraph 4 (figure S12)
The in-field gain is positively correlated with the out-of-field firing rate (rho = 0.17, P < 1e-5) and with the home-cage firing rate of the neuron (rho = 0.25, P < 1e-7).
This in-field gain was positively correlated with both the out-of-field firing rate and the home-cage firing rate of the neuron
Main text, paragraph 4 (figure S12)
What the paper reports
- in-field gain against out-of-field firing rate: ρ = 0.17, p < 10⁻⁵
- in-field gain against home-cage firing rate: ρ = 0.25, p < 10⁻⁷
Over 80 fields, rho is -0.018 (p = 0.87) for the out-of-field rate and -0.063 (p = 0.58) for the home-cage rate, both outside tolerance. With one field per cell, rho is 0.131 for the out-of-field rate (within tolerance) and -0.003 for the home-cage rate.
How the test differed from the paper’s method
- Two sessions of one mouse; 80 fields against 553.
Not reproducedMain text, paragraph 5; Figure 3A
Light responses in the home cage before the track were stronger in place cells than in non-place cells (P < 1e-4, Kruskal-Wallis test).
Light responses in place cells, tested in the home cage before the track, were significantly stronger than in non-place cells
Main text, paragraph 5; Figure 3A
What the paper reports
- Kruskal-Wallis test, p < 10⁻⁴
The PreStim light response (best uLED) has a median of 1.90 Hz in 72 place cells and 1.03 Hz in 19 non-place cells, higher in place cells but not significantly (Kruskal-Wallis p = 0.19; z-scored p = 0.25). It is significant in sess9 (p = 0.027) and not in sess12 (0.94 against 1.19 Hz, p = 0.85). Within halves of the baseline rate neither difference is significant (p = 0.6 and 0.2).
How the test differed from the paper’s method
- Two sessions of one mouse; 19 non-place cells.
- Place cells as in figs11-place-cell-fraction.
Not reproducedMain text, paragraph 5; Figure 3, B and C
Optogenetic depolarization revealed place fields in the majority of non-place cells, 289 of 417 (69.3%).
optogenetic depolarization revealed place fields in the majority of non-place cells (Fig. 3, B and C; 69.3%, 289 of 417
Main text, paragraph 5; Figure 3, B and C
Under reading (a), 7 of 9 light-responsive non-place cells (77.8%, 95% interval 40.0 to 97.2%) have a light field, 1.6 points above the tolerance of 69.3 plus or minus 6.9; under reading (b), 6 of 19 non-place cells (31.6%, 12.6 to 56.6%), below it and above the 15.8% found in control maps thinned at random to the time of the light maps. Reading (a) rests on 9 cells and its interval includes the paper's value. Its light maps use only each cell's own uLEDs (2.6% to 6.2% of lap time); control maps thinned to that time give a field in 31.7% of draws on average over the 9 cells.
How the test differed from the paper’s method
- Two sessions of one mouse; 19 non-place cells against 417.
- The paper's denominator and its rule for an induced field are in its unavailable Methods; two readings are shown.
Not reproducedFigure 3F
Place fields during light stimulation were more stable between the first and second halves of the session than during control epochs, for both true place fields and unmasked place fields (P < 1e-9 and P < 1e-19, two-way ANOVA).
Place fields during light stimulation were more stable for both true place fields and unmasked place fields
Figure 3F
What the paper reports
- true place fields: two-way ANOVA, p < 10⁻⁹
- unmasked place fields: two-way ANOVA, p < 10⁻¹⁹
Light maps are not more stable than control maps between laps 11-60 and 71-120 (place fields 0.664 against 0.714, light higher in 28 of 70, p = 0.058; unmasked fields 0.187 against 0.527, 6 of 14, p = 0.39). Against control maps from as many 20 ms control windows as light windows, place fields 0.664 against 0.602 (p = 0.68) and unmasked fields 0.187 against 0.293 (p = 0.67). Control maps from stimulated laps only give the same medians (p = 0.059 and 0.39), as they must, since dark windows lie only next to deposited pulses. The two-way ANOVA finds an effect of condition (p = 0.046), with light the less stable by the medians.
How the test differed from the paper’s method
- Control maps use the windows dark under the stated protocol (19% to 20% of lap time); the paper's control epochs were random 20 ms intervals between pulses, shown as a time-matched variant.
- Wilcoxon tests in place of the paper's two-way ANOVA, which is shown as a variant.
Not reproducedMain text, paragraph 7; Figure 4, C and D (legend panel D)
With light-induced spikes, the relationship between SPW-R cofiring and spatial overlap appears for pairs that include non-place cells (P < 1e-5, Spearman correlation).
during optogenetic stimulation, the relationship between cofiring during SPW-Rs and spatial overlap was revealed for unmasked place fields of non-place field pairs (Fig. 4C).
Main text, paragraph 7; Figure 4, C and D (legend panel D)
What the paper reports
- Spearman correlation, p < 10⁻⁵
Over 231 pairs of light-responsive place and non-place cells, cofiring is not significantly correlated with the overlap of light maps (rho = 0.075, p = 0.25; sess9 0.108, p = 0.16; sess12 -0.062, p = 0.65). With control maps the same pairs give rho = 0.110 (p = 0.094).
How the test differed from the paper’s method
- Two sessions of one mouse.
Partially reproducedMain text, paragraph 2
CA1 pyramidal neurons were recorded and probed in four CaMKIIa-Cre::Ai32 mice, 822 pyramidal neurons in all, 43.3 plus or minus 8.37 per session.
we recorded and probed large numbers of CA1 pyramidal neurons simultaneously in freely moving ... n = 822 pyramidal neurons in four mice; 43.3 ± 8.37 pyramidal neurons per session
Main text, paragraph 2
Under reading (a), all 28 sessions, 4 mice and 48.2 putative pyramidal cells per session (SD 12.18) match, but the total is 1351 against 822. Under reading (b), the 22 sessions naming the uLED protocol, 3 mice, 1047 cells and 47.6 per session. 822 cells at 43.3 per session would be about 19 sessions. With thresholds of 2.5 and 10 Hz the total is 1205 or 1441.
How the test differed from the paper’s method
- Pyramidal cells are units with a baseline rate below 5 Hz, as the files carry no cell type; the paper classified cells by other features.
- The paper does not say which sessions it used; two readings are shown.
Partially reproducedMain text, paragraph 2; Figure 1C
uLEDs were driven with 20 ms pulses at random sites with randomly variable 20 to 40 ms offsets, so that the stimulation of each site recurred at about 0.3 to 0.6 s intervals.
μLEDs were activated (0.02 to 0.1 μW, 20 ms duration) with randomly variable (20 to 40 ms) offsets so that stimulation of each site reccurred at ~0.3- to 0.6-s intervals
Main text, paragraph 2; Figure 1C
Pulses last 19.87 ms (sess9) and 19.63 ms (sess12). The median interval between pulses of one uLED is 0.281 to 0.383 s for the four uLEDs with at least 1000 pulses, within 0.27 to 0.66 s. The median offset from the end of one pulse to the start of the next is 60.4 and 80.0 ms, outside 18 to 44 ms; 31.8% and 30.2% of offsets fall within 20 to 40 ms, and the 95th percentiles are 241 and 328 ms. Most pulses are not in the files (5.76 and 7.50 deposited pulses per s in PreStim against about 17 to 25 implied by the protocol; in sess9 the offsets fall only near multiples of 20 ms), so the longer offsets span missing pulses and the protocol's offsets cannot be measured from the files.
How the test differed from the paper’s method
- Two sessions of 28, the only ones with pulse times.
- The files hold only part of the pulses, so the offsets between pulses are measured on the deposited ones.
Partially reproducedMain text, paragraph 3 (figure S10)
The firing-rate change of pyramidal neurons during SPW-Rs is negatively correlated with their baseline firing rate (rho = -0.19, P < 1e-7).
the negative correlation between firing-rate change during SPW-R and baseline firing rates of neurons
Main text, paragraph 3 (figure S10)
What the paper reports
- ρ = −0.19, p < 10⁻⁷
Over 1166 putative pyramidal cells of 24 sessions, the log2 ratio of the rate inside ripples to outside is negatively correlated with the baseline rate (rho = -0.437, p = 1.8e-55). It is negative in every subject (-0.37 to -0.71) and every session, and significant in all sessions but three (fCamk1 sess13 p = 0.12, fCamk3 sess13 p = 0.29, fCamk5 sess14 p = 0.81). This is stronger than -0.19 and outside the tolerance of 0.068. The difference reading gives rho = -0.002 (p = 0.95). Without the two sessions in the analysis whose ripples fail the clock check (the third has under 50 first-epoch ripples), n = 1055 and rho = -0.468; in the 22 sessions whose first epoch is labelled BaselinePre, -0.450; against the rate outside ripples, -0.466.
How the test differed from the paper’s method
- The paper's measure of rate change is in the unavailable supplement; two readings were fixed before the analysis and they disagree.
- The tolerance is the sampling half-width at n = 822, not 10% of the value.
Partially reproducedMain text, paragraph 4 (figure S11)
More than half of the pyramidal neurons were place cells, 73% of light-responsive and 71% of non-responsive neurons, with no difference between them (P = 0.90, chi-squared test).
more than half of the pyramidal neurons were classified as place cells [73% and 71% of light-responsive and nonresponsive neurons, respectively; P = 0.90, χ2 test
Main text, paragraph 4 (figure S11)
What the paper reports
- χ2 test, p = 0.9
48 of 57 light-responsive (84.2%, 95% interval 72.1 to 92.5%) and 24 of 34 non-responsive (70.6%, 52.5 to 84.9%) putative pyramidal cells are place cells; the paper's chi-squared test finds no difference (p = 0.20), as in the paper. The non-responsive fraction is within tolerance, the responsive one above it. Per session 83% against 56% (sess9) and 86% against 83% (sess12). Over all putative pyramidal cells 79.1% are place cells. With all time without a deposited pulse as control time and the earlier field rule (the round-1 analysis) the fractions are 78.9% and 52.9% with p = 0.018; the control time alone changes 5 cells, the field rule alone 1, both 11. Some non-responsive cells may respond to uLEDs whose pulses are not in the files.
How the test differed from the paper’s method
- Two sessions of one mouse.
- Place fields follow a port of buzcode's bz_findPlaceFields1D with its defaults, on control maps from the windows dark under the stated protocol (the 20 ms before each deposited onset and after each offset), since most pulses are not in the files; the paper's standard definition is in its unavailable Methods. The files do not follow the protocol exactly (3.2% and 3.8% of deposited offsets in PreStim are under 20 ms), so missing pulses may fall in some of these windows.
Partially reproducedMain text, paragraph 5; Figure 3, C and E
The spatial location of light-induced spikes matches that of spikes without stimulation, both for place fields of place cells (P < 1e-40) and for unmasked place fields of non-place cells, whose sparse control spikes form ghost fields (P < 1e-10).
We found a robust correlation between the spatial location of induced place field spikes and the sparse spikes of non-place cells in the absence of stimulation (Fig. 3, C and E
Main text, paragraph 5; Figure 3, C and E
What the paper reports
- place fields of place cells: χ2 test against 500 shuffles, p < 10⁻⁴⁰
- unmasked place fields of non-place cells: χ2 test, p < 10⁻¹⁰
For 70 field directions of light-responsive place cells the light peak follows the control peak (Pearson r = 0.806, p = 3.9e-17). For 14 light field directions of 7 non-place cells r = 0.321 (p = 0.26). In the shuffle variant, 35.7% of unmasked peaks lie within 4.4 cm of the control peak against 14.6% for shuffled pairings (p = 0.014), which is closer to the paper's test against shuffles. 8 of the 14 unmasked field directions come from sess9.
How the test differed from the paper’s method
- Pearson correlation of peak positions in place of the paper's chi-squared test against 500 shuffles, whose details are in the unavailable Methods; a shuffle test is shown as a variant.
Partially reproducedFigure 3Gverifier disagreed at first
Spatial information of control and light-stimulated epochs is correlated, and the light-boosted increase is stronger for unmasked place fields of non-place cells than for place cells (P < 1e-15, Kruskal-Wallis test).
Correlation of spatial information (Bits/spike) between control and light-stimulated epochs ... Light-boosted effect was stronger for unmasked place fields of non-place cells than for place cell place fields
Figure 3G
What the paper reports
- correlation of control and light spatial information, first of the two values printed: KW test, p < 10⁻⁶²
- correlation of control and light spatial information, second of the two values printed: KW test, p < 10⁻⁵⁸
- light-boosted effect, unmasked place fields against place cell place fields: KW test, p < 10⁻¹⁵
Control and light spatial information are correlated for place fields (rho = 0.655, p = 7.6e-10) and for unmasked fields (rho = 0.574, p = 0.032). The increase is larger for unmasked fields (median 0.03 against -0.03 bits/spike, Kruskal-Wallis p = 0.039), far from the paper's P < 1e-15. Against time-matched control maps both correlations hold (place rho = 0.501, p = 1e-05; unmasked rho = 0.609, p = 0.021), but the increase is negative in both groups (place -0.10, unmasked -0.17) and does not differ (p = 0.3); as a ratio it does not differ either (p = 0.14). The paper's control epochs are random 20 ms intervals between the light pulses, which the time-matched variant follows most closely, and the dark-window control maps are themselves a revision of the criterion's control (all time with no uLED on). Part 1 holds and part 2 does not. Unmasked fields are chosen for a light field and no control field, which favours a larger increase by construction; the paper defines its groups the same way. Changed from reproduced after verification round 3 agreed.
How the test differed from the paper’s method
- Control maps use the windows dark under the stated protocol; time-matched control windows are a variant, under which the larger increase in unmasked fields does not hold.
ReproducedMain text, paragraph 2; Figure 1E
Of 822 pyramidal neurons, 611 responded to light from the uLEDs.
Of 822 neurons, 611 responded unequally to the three neighboring μLEDs
Main text, paragraph 2; Figure 1E
Under reading (b), all stimulation epochs, 66 of 91 putative pyramidal cells (72.5%, 95% interval 62.2 to 81.4%) respond to at least one uLED. Under reading (a), the PreStim epoch, 57 of 91 (62.6%, 51.9 to 72.6%), outside tolerance. Of 364 unit and uLED tests in PreStim, 68 pass all three parts of the test; on sham onsets (jittered by up to 200 ms, or moved into BaselinePre) none of 364 passes. For reading (b), with the onsets of all stimulation epochs jittered by up to 200 ms, none of 364 tests passes either. No putative pyramidal cell on shank Group3 responds (0 of 17), and that shank's uLEDs are likely among those whose pulses are not in the files. Without Group3, 57 of 74 (77.0%) under (a), within tolerance, and 66 of 74 (89.2%) under (b), above it. The criterion lists (a) first but only (b) matches, so the measured value is that of (b).
How the test differed from the paper’s method
- Two sessions of one mouse (91 putative pyramidal cells), not 822 cells.
- The response test is the one in the first author's later code (HippoCookBook getuLEDResponse.m), with 500 bootstrap sets drawn on a 1 ms grid and shared across units, and a minimum of 1000 pulses per uLED in place of 2000; the paper's own test is in its unavailable Methods.
- Which pulses the paper tested is not stated; two readings are shown and the claim matches under reading (b) only.
- Cells near uLEDs whose pulses are not in the files cannot be tested for a response to them.
ReproducedMain text, paragraph 3; Figure 1, F to I
Light-induced spike responses of individual pyramidal cells decreased during sharp-wave ripples (n = 485 neurons, P < 1e-55, Wilcoxon paired signed-rank test).
light-induced spike responses in individual pyramidal cells decreased during SPW-Rs (ΔRate; Fig. 1, F to I).
Main text, paragraph 3; Figure 1, F to I
What the paper reports
- Wilcoxon paired signed-rank test, p < 10⁻⁵⁵ (n = 485 neurons)
In 57 light-responsive putative pyramidal cells, light minus control rate is 0.30 Hz (median) in windows overlapping ripples and 2.68 Hz outside, lower inside in 49 of 57 (Wilcoxon p = 6.8e-09), and in each session (p = 7.8e-06 and 9.5e-07). As a ratio, 1.25 inside and 2.89 outside (53 of 56, p = 8.6e-10). The paper's n of 485 and P < 1e-55 cannot be reached with two sessions. The control windows, the 20 ms before each onset, are dark under the stated protocol, so the missing pulses do not enter them.
How the test differed from the paper’s method
- Two sessions of one mouse.
- Ripples are the deposited ripple intervals; a window counts as inside a ripple when it overlaps one.
- Control windows are the 20 ms before each pulse with no uLED on.
ReproducedMain text, paragraph 4; Figure 2, C to E
The light-induced rate increase is higher within than outside the place field (n = 553 place fields, P < 1e-115, Wilcoxon test).
The induced rate increase was higher within than outside the place field (Fig. 2E and fig. S12).
Main text, paragraph 4; Figure 2, C to E
What the paper reports
- Wilcoxon test, p < 10⁻¹¹⁵ (n = 553 place fields)
Over 80 control place fields of 48 light-responsive putative pyramidal cells, gain is 3.95 Hz in the field and 1.37 Hz outside (medians), higher in the field for 61 of 80 (Wilcoxon p = 1e-08) and in each session (p = 9.5e-07 and 0.0018). As a ratio of light to control the in-field value is lower (2.19 against 2.77, p = 4.3e-05), so the increase is larger in hertz but not relative to the control rate.
How the test differed from the paper’s method
- Two sessions of one mouse; 80 fields against 553.
- Control rates come from the windows dark under the stated protocol.
ReproducedFigure 4C (legend); Main text, paragraph 7; Figure 4, B and C
Cofiring of place cell pairs during SPW-Rs in the home cage is positively correlated with their spatial overlap on the track (P < 1e-27), while pairs of a place cell and a non-place cell show no such relationship (P = 0.11).
SPW-R cofiring was positively correlated with spatial overlap in place cell pairs ... but not in pairs with place and non-place cell (non-PC) partners (P = 0.11).
Figure 4C (legend); Main text, paragraph 7; Figure 4, B and C
What the paper reports
- place cell pairs: Spearman correlation, p < 10⁻²⁷
- pairs of a place cell and a non-place cell: Spearman correlation, p = 0.11
Over 1264 place cell pairs, ripple cofiring is correlated with spatial overlap (rho = 0.060, p = 0.032), so part 1 holds, weakly and in sess9 only (0.119, p = 0.0015; sess12 0.019, p = 0.66). Over 698 place and non-place pairs the paper's test finds no correlation (rho = 0.062, p = 0.1), so part 2 holds, but the coefficient is as large as for place cell pairs. Correlation of participation per ripple gives 0.054 (p = 0.056) and 0.072 (p = 0.058).
How the test differed from the paper’s method
- Two sessions of one mouse.
- Cofiring as the Pearson correlation of spike counts per deposited ripple, a choice made here; the paper's measure is in its unavailable Methods.

Not tested in a notebook 6

2 data missing from the dataset, 1 metadata insufficient, 3 methods underspecified

BlockedFigure 1J, Figure 2F, Figure 3D; Main text, paragraphs 3 and 4· Data missing from the dataset
Stronger light (three intensities) decreased the light-induced response during SPW-Rs, increased the in-field gain of place cells several-fold, and increased the in-field gain of unmasked fields (Figure 1J, Figure 2F, Figure 3D; Friedman tests).
Increasing Vm depolarization decreased the light-induced response during SPW-Rs (Fig. 1J) ... Increasing depolarization of Vm by stronger light intensity increased the in-field gain several-fold (Fig. 2F).
Figure 1J, Figure 2F, Figure 3D; Main text, paragraphs 3 and 4
What the paper reports
- response during SPW-Rs across light intensities, correlation (Figure 1J): ρ = −0.55, p < 10⁻⁵⁷
- response during SPW-Rs across light intensities, all comparisons (Figure 1J): Friedman test, p < 10⁻⁹
- in-field gain of place cells across light intensities, correlation (Figure 2F): ρ = 0.24, p < 10⁻⁶
- in-field gain of place cells across light intensities (Figure 2F): Friedman test, p < 10⁻⁸
- in-field gain of unmasked fields across light intensities, all comparisons (Figure 3D): Friedman test, ρ = 0.38, p < 10⁻⁵
The pulse series hold one value per uLED in each of the two sessions with pulses (19 in sess9, 62623 to 63599 in sess12, stated as watts), so no pulse has an intensity level, and the other 26 sessions have no pulse series. The paper's other named data location, the Buzsaki Lab Databank, serves data through Globus with an account and no pinned identifier.
BlockedMain text, paragraph 3; Figure 1, K to M· Data missing from the dataset
Intracellular recordings in which the membrane potential was varied reproduce the decreased gain during SPW-Rs (five cells in anesthetized rats and five in head-fixed mice, P = 0.002).
more directly by intracellular experiments, in which Vm was systematically varied (Fig. 1, K to M), reproducing the effect seen with optogenetic Vm depolarization (Fig. 1I)
Main text, paragraph 3; Figure 1, K to M
What the paper reports
- Wilcoxon paired signed-rank test, p = 0.002 (n = five cells from five anesthetized rats and five cells from four head-fixed mice)
The dandiset holds extracellular recordings of four mice only; the intracellular recordings in rats and head-fixed mice are not in it. The lab's data page lists this dandiset for the paper and otherwise points to a Globus endpoint without a pinned identifier.
BlockedMain text, paragraph 3 (figure S9)· Metadata insufficient
During SPW-Rs, excitatory neurons increased their firing rates more than inhibitory neurons.
During sharp-wave ripples (SPW-Rs), excitatory neurons increased their firing rates more than inhibitory neurons (fig. S9)
Main text, paragraph 3 (figure S9)
The units carry no cell type, and the no-raw-data files hold no waveforms. A rate threshold separates cells by the very quantity the claim compares, so it was not used for this claim. Waveforms could be taken from the raw signal, but the full files are 17 to 54 GB each and six of them have no raw signal. As a proxy shown in the notebook, units at or above 5 Hz raise their rate inside ripples less than putative pyramidal cells (median log2 ratio 0.75 against 1.19, p = 0.00065); since the ripple gain falls with baseline rate within putative pyramidal cells alone (figs10), this split would show the same without interneurons, so it does not test the claim.
BlockedMain text, paragraph 6; Figure 3H· Methods underspecified
Decoding of position is most accurate from light-boosted spikes of place cells, and light-induced spikes of non-place cells predict position better than control spikes of place cells (P = 0.001, Tukey test).
The root mean squared error of the decoded position was highest for the sparse non-place cell spikes and lowest for light-boosted spikes of place cells. The induced spikes of non-place cells more accurately predicted the mouse's position on the track
Main text, paragraph 6; Figure 3H
What the paper reports
- Tukey test, p = 0.001
The decoder, its spatial bins, time windows and cross-validation are described in the supplement, which could not be obtained; the main text and legend do not fix them. The data for it (two sessions with laps and pulses) are in the dandiset.
BlockedMain text, paragraph 7; Figure 4, E and F· Methods underspecified
ICA assemblies of place cells in the home cage show higher spatial correlation than chance, mixed assemblies of place and non-place cells do not, and with unmasked place fields they reach the level of place-cell assemblies.
Assembly members of place cells, but not of mixtures of place and non-place cells, showed higher spatial correlation than chance (Fig. 4E). However, when spikes of unmasked place fields were considered, they expressed spatial correlation at the level of real place cells
Main text, paragraph 7; Figure 4, E and F
What the paper reports
- assemblies of only place cells against mixed assemblies: two-way ANOVA, p = 0.006
- interaction of assembly type and light stimulation: two-way ANOVA, p = 0.02
The ICA assembly detection (bin size, significance of components) and the chance level for spatial correlation are in the unavailable supplement. The legend gives only the member threshold of 2 SD. The data are in the dandiset for two sessions.
BlockedMain text, paragraph 7; Figure 4, G and H· Methods underspecified
Sequential firing of place cells is correlated with spike sequences during SPW-Rs, and the fraction of SPW-Rs with significant trajectories increases when unmasked place fields are included in the template (P < 1e-4, Friedman test).
Sequential firing of place cells was correlated with spike sequences during SPW-Rs (Fig. 4G) ... The fraction of SPW-R events with significant virtual track trajectories increased when unmasked place fields were also included for the construction of the place field sequence template
Main text, paragraph 7; Figure 4, G and H
What the paper reports
- fraction of SPW-Rs with significant trajectories across templates: Friedman test, p < 10⁻⁴
- template with unmasked place fields of non-place cells: Tukey test, p < 10⁻⁴
The Bayesian decoding of ripples, the template construction and the shuffle are in the unavailable supplement; the legend gives only 500 shuffles. The data are in the dandiset for two sessions.

Findings about the data

What attempts found about the dataset itself, for its owner and the archive.

Data missingLight pulse times are deposited for 2 of 28 sessions (fCamk1 sess9 and sess12). Twenty other sessions name uLED stimulation in their epochs but hold no pulse series, so their light responses cannot be computed. Laps are also in these two sessions only.
Metadata errorThe OptogeneticSeries are stated in watts but hold one value per uLED, 19 in sess9 and 62623 to 63599 in sess12, not a light power (the paper gives 0.02 to 0.1 uW). No light intensity per pulse is stored, so the paper's three intensities cannot be recovered.
Data missingThe files hold pulse series for 6 of the probe's 12 uLEDs (Site3 to Site8), two of them with only 120 to 221 pulses, and most pulses of the protocol are missing. In PreStim the deposited pulses come at 5.76 and 7.50 per s, where the stated protocol implies about 17 to 25; in fCamk1 sess9 the offsets between deposited pulses fall only near multiples of 20 ms, the gaps left by missing pulses. No putative pyramidal cell on shank Group3 responds to any deposited uLED. Time without a deposited pulse therefore cannot be taken as dark.
OtherEvery session is deposited twice, as a full file and a no-raw-data file; in all 28 sessions the two hold the same units, spike times, ripples and position. The full file of fCamk3 sess20 is named sub-fCamk3_behavior+ecephys+image.nwb, without its session.
Data missingThe full file of fCamk3 sess17 is 28 MB and holds 378 s of raw signal and 6850 s of LFP of a 34621 s session. The six full files of fCamk1 sess13 to sess19 hold the LFP but no raw signal.
Description missingUnits carry no cell type and the no-raw-data files no waveforms, so pyramidal cells and interneurons cannot be told apart as in the paper.
Metadata errorsession_start_time is 2016-03-15 in every file, while the session ids date the recordings to 2020 and 2021.
Metadata errorThe linearized position holds values from 0 to 110 cm (the track length) but has a conversion factor of 100, which would put it at 0 to 110 m.
Description missingSix sessions (fCamk2 sess1 to sess4, fCamk3 sess13, fCamk5 sess10) name their epochs only by a time stamp, without behavioral paradigm or manipulation. fCamk2 sessions have no position and 0 to 1110 ripples.
Selection not documentedThe dandiset holds 28 sessions and 1351 units with a baseline rate below 5 Hz, where the paper reports 822 pyramidal neurons at 43.3 per session (about 19 sessions). It does not say which sessions the paper used. 14 sessions include CNO or DMSO epochs, which the paper does not describe.
OtherIn fCamk3 sess13, fCamk3 sess17 and fCamk5 sess10 the deposited ripple intervals mark population bursts weakly (population rate 1.2 to 1.98 times that 1 s later, against at least twice in the other 22 sessions with ripples). fCamk5 sess10 has 217 events with a median length of 109 ms.
Paper inconsistentThe paper gives randomly variable 20 to 40 ms offsets between pulses, the files' description 40 to 60 ms. Measured onset to onset, 30% to 32% of the deposited intervals fall in 40 to 60 ms; measured end to start, 30% to 32% fall in 20 to 40 ms, and most others span missing pulses.
Methods not availableThe paper's Materials and Methods are in its supplement. This attempt could not obtain the supplement from PMC or the publisher, and the analysis code the paper names (buzcode) is a general toolbox without scripts for its figures.
Paper inconsistentThe paper reports 822 pyramidal neurons of which 73% of light-responsive and 71% of non-responsive neurons were place cells, which leaves about 230 non-place cells, but gives the unmasked fraction as 289 of 417 non-place cells.
Description missingThe units table of some files lacks the shank column (group_id); columns are spike_times, unit_name, clu_id and, in the others, group_id.

Notebooks

Every registered entry that uses this dataset. An entry can hold several notebooks, and can use more than one dataset.

Reproduction Pulsed optogenetics in hippocampal CA1 (Valero et al. 2022)

Tests the findings of Valero, Zutshi, Yoon and Buzsaki (2022) on dandiset 000568, which holds 28 sessions of CA1 units recorded with uLED probes in four CaMKIIa-Cre::Ai32 mice. Pulse times and laps are in two sessions only, so the light responses during ripples, theta and place fields are tested on those two; the ripple modulation of firing is tested on all sessions. The intracellular recordings and the light intensity levels are not in the dandiset. All files

Reproducing Valero et al. (2022) from dandiset 000568
reproduce_valero_2022.ipynbExecuted, with outputs · Source

Verification

Round 1
2026-10-17Agreed with 22 of 22 outcomes. Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook). Reviewed: Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper (PMC author manuscript). The verifier did not open NWB files; it tested find_fields and a simulated pulse protocol on synthetic inputs and read the archive's asset list. Its report had no attempt record and gave its own outcome for each claim; all 22 agree with the record as it then stood. The revision changed five outcomes, which round 2 reviews.
Round 2
2026-10-17
Agreed with 21 of 22 outcomes. Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook). Reviewed: Round 2. The full executed notebook after the round-1 revision, with its conclusions and summary, the helper module, the claims file and the attempt record, with the paper (PMC author manuscript, saved as paper/PMC9632609_bioc.json and paper/PMC9632609.txt). It read the new find_fields but could not run it, as numpy was not installed. Report in transcripts/000568/verifier-2-report.md. Points not tied to one claim were also answered. The dark-window premise (round-2 remaining point 4) is now printed in the data check (3.8% and 3.2% of deposited offsets in PreStim under 20 ms) and stated in cell 12, the figs11 deviations and the summary. Point 3 (two sessions of one mouse) needs no change beyond what the notes state. Point 5 (Methods) cannot be answered, as the supplement is still unavailable.
- fig3g-spatial-information: the verifier’s outcome was “Partially reproduced”. Part 2 rests on p = 0.039 with dark-window control maps. Against time-matched control the increase is negative in both groups and does not differ (p = 0.3). The paper says random intervals (20 ms) between the light pulses served as control epochs, which the time-matched variant follows most closely. The criterion fixed time when no uLED is on, which the revision already replaced, so the main control maps are not the pre-registered ones either, and the selection bias still favours part 2.
Round 3
2026-10-17Agreed with 1 of 1 outcomes. Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook). Reviewed: Round 3. The one proposed change of outcome (fig3g-spatial-information) and the analysis behind it in the executed notebook after the round-2 revision (cells 51, 59 and 60), with the paper text saved in round 2. Nothing else was reviewed. Report in transcripts/000568/verifier-3-report.md.

Method differences

How the tests differed from the paper’s method or data, and the claims each applies to.

Two sessions of one mouse.fig1i-swr-decrease fig2b-theta-trough-gain figs11-place-cell-fraction fig4c-swr-cofiring-place-pairs fig4d-light-unmasked-cofiring
Two sessions of one mouse; 80 fields against 553.fig2e-infield-gain figs12-gain-rate-correlations
Pyramidal cells are units with a baseline rate below 5 Hz, as the files carry no cell type; the paper classified cells by other features.cohort-counts
The paper does not say which sessions it used; two readings are shown.cohort-counts
Two sessions of 28, the only ones with pulse times.fig1c-pulse-protocol
The files hold only part of the pulses, so the offsets between pulses are measured on the deposited ones.fig1c-pulse-protocol
Two sessions of one mouse (91 putative pyramidal cells), not 822 cells.fig1e-responsive-fraction
The response test is the one in the first author's later code (HippoCookBook getuLEDResponse.m), with 500 bootstrap sets drawn on a 1 ms grid and shared across units, and a minimum of 1000 pulses per uLED in place of 2000; the paper's own test is in its unavailable Methods.fig1e-responsive-fraction
Which pulses the paper tested is not stated; two readings are shown and the claim matches under reading (b) only.fig1e-responsive-fraction
Cells near uLEDs whose pulses are not in the files cannot be tested for a response to them.fig1e-responsive-fraction
Ripples are the deposited ripple intervals; a window counts as inside a ripple when it overlaps one.fig1i-swr-decrease
Control windows are the 20 ms before each pulse with no uLED on.fig1i-swr-decrease
The paper's measure of rate change is in the unavailable supplement; two readings were fixed before the analysis and they disagree.figs10-swr-gain-vs-baseline-rate
The tolerance is the sampling half-width at n = 822, not 10% of the value.figs10-swr-gain-vs-baseline-rate
The LFP channel (largest ripple power), the theta band (6 to 10 Hz) and the half-cycle split are choices made here; the paper's are in its unavailable Methods.fig2b-theta-trough-gain
Place fields follow a port of buzcode's bz_findPlaceFields1D with its defaults, on control maps from the windows dark under the stated protocol (the 20 ms before each deposited onset and after each offset), since most pulses are not in the files; the paper's standard definition is in its unavailable Methods. The files do not follow the protocol exactly (3.2% and 3.8% of deposited offsets in PreStim are under 20 ms), so missing pulses may fall in some of these windows.figs11-place-cell-fraction
Control rates come from the windows dark under the stated protocol.fig2e-infield-gain
Two sessions of one mouse; 19 non-place cells.fig3a-place-cells-more-excitable
Place cells as in figs11-place-cell-fraction.fig3a-place-cells-more-excitable
Two sessions of one mouse; 19 non-place cells against 417.fig3c-unmasked-fields
The paper's denominator and its rule for an induced field are in its unavailable Methods; two readings are shown.fig3c-unmasked-fields
Pearson correlation of peak positions in place of the paper's chi-squared test against 500 shuffles, whose details are in the unavailable Methods; a shuffle test is shown as a variant.fig3e-ghost-fields
Control maps use the windows dark under the stated protocol (19% to 20% of lap time); the paper's control epochs were random 20 ms intervals between pulses, shown as a time-matched variant.fig3f-light-stability
Wilcoxon tests in place of the paper's two-way ANOVA, which is shown as a variant.fig3f-light-stability
Control maps use the windows dark under the stated protocol; time-matched control windows are a variant, under which the larger increase in unmasked fields does not hold.fig3g-spatial-information
Cofiring as the Pearson correlation of spike counts per deposited ripple, a choice made here; the paper's measure is in its unavailable Methods.fig4c-swr-cofiring-place-pairs

Provenance

Attempt record: 000568-valero-2022-01
Paper: Probing subthreshold dynamics of hippocampal neurons by pulsed optogenetics
Date: 2026-10-17
Made by: An agent, run by CatalystNeuro
Dataset: DANDI:000568
Version: 0.230705.1633 (doi:10.48324/dandi.000568/0.230705.1633)
Run on: GitHub Actions
Harness: Claude Code (GitHub Actions)
Model: claude-opus-5-5
Protocol: pilot-7

Transcripts of the agent runs

Each run’s prompt, messages and tool calls, with long output cut and the text of the paper left out, and its final report.

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