Preconfigured dynamics in the hippocampus are guided by embryonic birthdate and rate of neurogenesis (DANDI:000552)

Claims

From the paper Preconfigured dynamics in the hippocampus are guided by embryonic birthdate and rate of neurogenesis

Reproducing Huszar et al. (2022) from dandiset 000552 12

Notebook reproduce_huszar_2022.ipynb

Not reproducedMethods, Unit isolation and classification; Extended Data Figure 2a
The dataset includes 9,471 well-isolated units, 7,411 putative pyramidal cells and 2,060 putative interneurons.
The dataset includes a total of 7,411 well-isolated putative pyramidal cells and 2,060 putative interneurons ... for isolated units (n = 9,471)
Methods, Unit isolation and classification; Extended Data Figure 2a
8,201 units in 65 of 104 files, below the tolerance of 8,524 to 10,418. Six mice (e13_1f1, e13_1m1, e14_1m1, e15_4m1, e15_4m2, e15_5m1; 39 files) have no units. Files with units hold 34 to 376 (median 99). The 5 Hz rule classes 87.8% as putative pyramidal cells, against the paper's 78.3%.
How the test differed from the paper’s method
- The pyramidal fraction uses a firing-rate rule, as the files hold no cell type.
Not reproducedMethods, Behavior, paragraph 1
On the figure-eight maze each trial was 205 cm long, position was tracked at 30 Hz, and animals ran at least ten trials along each arm in every session.
The length of each trial was 205 cm. ... at a frame rate of 30 Hz ... Animals were required to run at least ten trials along each arm (at least twenty trials total) within each session.
Methods, Behavior, paragraph 1
Median trial length 204.1 cm and tracking at 30.00 Hz in all 65 familiar recordings, both within tolerance. Only 38 of 65 sessions have at least ten trials on each visited arm (22 of 65 by expected arm), and 6 sessions have fewer than 20 trials (fewest 12), so neither the full nor the partial condition holds. The requirement may have applied to training, not to every recorded session.
How the test differed from the paper’s method
- Two readings of "trials along each arm" (visited and expected) were used; neither holds.
Not reproducedFigure 6c, bottom
Pairwise spatial ratemap correlations between pyramidal neurons are higher in novel environments (median 0.048) than in the familiar environment (median -0.045).
pairwise analysis revealed systematically higher spatial ratemap correlations in novel environments (Fig. 6c)
Figure 6c, bottom
What the paper reports
- two-sided Wilcoxon, p = 3.2 × 10⁻²⁸³ (n = 31,067 familiar and 41,991 novel pairs)
Median familiar -0.0530 over 327,656 pairs (within tolerance) and novel -0.0364 over 242,655 pairs (outside 0.018 to 0.078); rank-sum p = 0.67. Within each of the 9 sessions with a novel maze the novel median is higher than the familiar one (sign test p = 0.0039; rank-sum p < 0.05 within 7 of the 9 sessions), so the direction holds session by session; the pooled test, which the criterion names, is weighted by the sessions with most pairs; with familiar pairs only from those sessions the pooled test gives p = 0.1. Variants with all units (p = 0.38) or a 10 Hz rule (p = 0.66) agree; including the stem gives p = 3.5e-50 with novel higher. Per maze kind, novel medians run from -0.0548 to 0.0073.
How the test differed from the paper’s method
- All pairs of putative pyramidal cells, where the paper's pairs each include a light-responsive neuron (not identifiable in the files).
- Novel mazes are only the T-maze and linear tracks with position; the paper's novel pairs also come from open fields with two-dimensional maps.
Partially reproducedMethods, Implantation and recording, paragraph 2
The recordings comprise 92 sessions lasting 113.7 to 475.6 min (median 309.1 min), each including a homecage period of sleep and wake.
All recordings (92 sessions ranging in duration from 113.7 min to 475.6 min; median duration = 309.1 min) included a homecage period of sleep and wake.
Methods, Implantation and recording, paragraph 2
104 processed files, within 10% of the 96 sessions of Figure 1e and Figure 7f but not of the 92 of the Methods. Median duration 319.6 min (paper 309.1), range 113.7 to 494.2 min, all inside the widened range of 102.3 to 523.2 min; two files last exactly the paper's bounds (113.7 and 475.6 min). Without e15_13f1 and e16_3m2 there are 96 sessions with per-birthdate counts equal to Figure 1e (30, 24, 24, 18), range 113.7 to 475.6 min and median 309.9 min. Two files of e13_1f1 (200305, 200307) hold one Awake interval for the whole session and no scored sleep, so the statement that each session includes sleep fails for them; that part makes the outcome partial.
How the test differed from the paper’s method
- Session duration is the end of the last sleep-state or ripple interval; in 57 files the last spike falls 1.2 to 5.2 s later.
- The criterion named the sleep condition without saying which outcome its failure gives; with the count, median and range holding and the sleep condition failing in 2 of 104 files, the outcome is taken as partial.
- The session count was judged under two readings (92 and 96), as the paper gives both.
Partially reproducedResults, SBD pyramidal neurons exhibit overlapping place tuning, paragraph 3; Methods, Behavior, paragraph 2
The novel-environment cohort of three mice made 16 novel environment explorations in six distinct environments (two linear tracks, three open fields and one figure-eight maze).
Altogether, we obtained n = 16 novel environment explorations across animals. Six distinct novel environments were employed: two linear tracks, three open fields and one figure-eight maze.
Results, SBD pyramidal neurons exhibit overlapping place tuning, paragraph 3; Methods, Behavior, paragraph 2
Three mice with 9 novel explorations that have trials and position (3 T-maze runs of about 164 cm, 3 linear-track runs of 110 cm and 3 of 100 cm), against 16. The novel-cohort sessions also hold 7 epochs of 10 to 50 min without position that are not a session's last epoch, and the files hold no other position or video series for them. They are not counted; they would bring the count to 16, but they were picked after the data were seen and nothing in the files marks them as explorations. No open field has position.
Partially reproducedFigure 5e
Population firing-rate vectors at the same linearized position decorrelate between left and right trials once the animal leaves the common stem of the figure-eight maze (median correlations stem 0.93, turn 1 0.412, arm 0.372, turn 2 0.394).
Population firing rate vectors at linearized positions along the maze decorrelated between left and right trial types as soon as animals exited the common stem segment of the maze (Fig. 5e).
Figure 5e
What the paper reports
- Kruskal–Wallis, H = 7,278.3, d.f. = 3, p = 0 (n = 4,218, 2,109, 4,218 and 1,140 population vector pairs)
57 sessions of nine mice (the paper's bin counts, 4,218 stem bins, imply the same 57), with 28 to 242 putative pyramidal cells per session. Kruskal-Wallis H = 7632.7 (paper 7278.3), p = 0, stem highest. Stem 0.937 is within tolerance; turn 1 0.547, arm 0.492 and turn 2 0.465 are above the paper's 0.412, 0.372 and 0.394. The stem is the most correlated segment in every mouse. The medians depend strongly on the cell rule; at most 2 Hz gives 0.925, 0.387, 0.288, 0.306; at most 10 Hz gives 0.966, 0.787, 0.771, 0.746; all units 0.988, 0.948, 0.94, 0.921; no speed threshold 0.924, 0.589, 0.522, 0.492. With a 2.59 Hz rule, which classes the paper's fraction of units (0.783) as pyramidal, the medians are 0.928, 0.436, 0.343 and 0.357, all four within tolerance; the criterion fixed the 5 Hz rule, so this variant does not change the outcome. 51 of 11,685 bins had no value.
How the test differed from the paper’s method
- Putative pyramidal cells by session mean rate (at most 5 Hz), not by waveform and autocorrelogram; the files hold no cell type or waveforms.
- Speed from smoothed linearized position, not a Kalman filter.
Partially reproducedFigure 6d, right
Spatial information is lower in novel environments than in the familiar one (median 0.39 against 0.88 bits/s).
This latter difference may be due to lower spatial information content in novel environments (Fig. 6d)
Figure 6d, right
What the paper reports
- two-sided Wilcoxon, p = 8 × 10⁻¹¹⁶ (n = 2,544 neurons in the familiar and 3,443 in novel environments)
Familiar median 0.631 bits/s over 2,709 cells and novel 0.270 over 2,028 cell-maze values, rank-sum p = 1.5e-59, so information is lower in novel mazes as stated, but both medians are below the tolerances (0.792 to 0.968 and 0.351 to 0.429). The code's unweighted measure gives 0.646 and 0.285. By mouse, familiar 0.617 to 0.645; novel 0.083 to 0.337 on linear tracks and 0.282 to 0.608 on the T-maze.
How the test differed from the paper’s method
- Skaggs information over left and right maps of the whole linearized track, with putative pyramidal cells by firing rate; no open fields.
ReproducedResults, In vivo recordings from birthdated CA1 pyramidal neurons, paragraph 1; Methods, Implantation and recording, paragraph 1verifier disagreed at first
Chronic recordings were made from 17 adult mice (12 males, 5 females) electroporated at E13.5 (n = 4), E14.5 (n = 3), E15.5 (n = 6) and E16.5 (n = 4).
Chronic recordings were performed from n = 17 freely moving adult mice (12 males, 5 females; age 3–6 months; electroporated at: E13.5, n = 4; E14.5, n = 3; E15.5, n = 6; E16.5, n = 4)
Results, In vivo recordings from birthdated CA1 pyramidal neurons, paragraph 1; Methods, Implantation and recording, paragraph 1
17 mice, with E13.5 4, E14.5 3, E15.5 6 and E16.5 4, as the paper states. With each mouse's sex taken from most of its files, 12 males and 5 females, as the paper states. The sex field differs between files of two mice (e13_1f1 Female in 3 files and Male in 2; e13_1m1 Male in 9 and Female in 3), so reading only each mouse's first file gives 13 and 4. The ids, which carry f or m, also give 12 and 5.
How the test differed from the paper’s method
- The criterion took sex from the subject metadata without saying how to combine files that disagree; the value in most of a mouse's files is used, chosen after the per-file values were seen (the first round of this attempt read the first file and gave 13 and 4).
ReproducedFigure 2b legend; Methods, SPW-R detection
SPW-Rs were detected with duration limits of 20 to 200 ms, and their median duration across all recordings was 36.4 ms.
SPW-R duration limits were set to be between 20 and 200 ms. ... White dotted lines indicate the median duration of SPW-Rs across all recordings (36.4 ms).
Figure 2b legend; Methods, SPW-R detection
Median duration 36.0 ms over all 494,578 ripples pooled and 36.0 ms as the median of the 104 session medians (paper 36.4). All ripples last 20.0 to 199.2 ms, within the 20 to 200 ms limits. Per-mouse medians run from 29.6 to 40.0 ms.
How the test differed from the paper’s method
- Uses the ripples stored in the files; detection was not repeated.
ReproducedResults, SBD pyramidal neurons exhibit overlapping place tuning, paragraphs 1 and 3; Methods, Behavior, paragraphs 1 and 2
Nine mice (E13.5 n = 2, E14.5 n = 2, E15.5 n = 2, E16.5 n = 3) ran a spatial alternation task on a familiar figure-eight maze, and a cohort of three mice also explored novel environments.
A subset of n = 9 mice (E13.5, n = 2; E14.5, n = 2; E15.5, n = 2; E16.5, n = 3) was trained on a spatial alternation task in a figure-eight maze ... a subset of n = 3 mice (Supplementary Table 1) that underwent in utero electroporation was exposed to novel environments
Results, SBD pyramidal neurons exhibit overlapping place tuning, paragraphs 1 and 3; Methods, Behavior, paragraphs 1 and 2
11 mice have figure-eight trials. Under reading (b), the maze mice without e15_13f1 and e16_3m2 are nine, at E13.5 2, E14.5 2, E15.5 2 and E16.5 3, and three mice (e13_26m1, e15_13f1, e16_3m2) have novel recordings, so e13_26m1 is in both cohorts. Reading (a), disjoint cohorts of 12 mice, does not hold.
How the test differed from the paper’s method
- The paper calls the novel cohort separate; the reading that matches takes the overlap from the paper's code, recorded as an ambiguity.
ReproducedFigure 6c, top
Individual pyramidal neurons preserve their theta-related firing rates between the familiar and novel environments (Spearman rho = 0.7378, n = 2,544 neurons).
Individual pyramidal neurons preserved their theta-related firing rates across environments
Figure 6c, top
What the paper reports
- Spearman's correlation, ρ = 0.7378, p = 0 (n = 2,544 neurons)
Spearman rho = 0.726 over 2,038 putative pyramidal cells with a familiar and a novel rate (paper 0.7378 over 2,544), p = 0; per mouse 0.711 to 0.745, per session 0.586 to 0.826. Variants with all units, a 10 Hz rule or a 1.5 cm/s running threshold give 0.754 to 0.802. 679 cells of the 3 sessions without a novel maze have no novel rate. The running rate now ends each running stretch at the end of its trial (round 1 gave 0.734 with stretches that could span the gap between trials).
How the test differed from the paper’s method
- The rate is the firing rate while running at 5 cm/s or faster inside maze trials, in place of the rate in LFP theta cycles; the LFP is in the raw files of 8 of the 9 novel sessions but was not used.
- Novel mazes are only those with position; the open fields are not in the data.
- Putative pyramidal cells by firing rate.
ReproducedFigure 6d, left
Theta-related firing rates are slightly lower in novel environments than in the familiar one (median 0.69 against 0.77 Hz).
theta-related firing rates (Hz) in familiar (gray, n = 2,544 neurons, median = 0.77) and novel environments (black, n = 2,544, median = 0.69
Figure 6d, left
What the paper reports
- two-sided Wilcoxon, p = 0.0033 (n = 2,544 neurons in each environment)
Familiar median 0.794 Hz over 2,717 cells and novel 0.714 Hz over 2,038, both within tolerance of the paper's 0.77 and 0.69 Hz; rank-sum p = 0.041 (paper 3.3e-3). The difference is weak. The paired signed-rank test gives a median ratio of 0.942, p = 0.19; familiar from the sessions with a novel maze only gives p = 0.09; the variants (all units, 10 Hz rule, 1.5 cm/s threshold) give lower novel rates with p = 0.075 to 0.11. Novel is lower in two mice (0.722 against 0.883, 0.680 against 0.835) and slightly higher in e15_13f1 (0.734 against 0.729). Round 1 gave 0.958 and 0.799 Hz, p = 7e-06, with running stretches that could span the gap between trials and count its spikes but not its time; in 371 of 698 pairs of consecutive trials the animal was running at the end of one and the start of the next.
How the test differed from the paper’s method
- Running rate in place of the rate in LFP theta cycles.
- Putative pyramidal cells by firing rate; no open fields.

Not tested in a notebook 23

22 data missing from the dataset, 1 methods underspecified

BlockedExtended Data Figure 2a· Data missing from the dataset
664 of 7,411 putative pyramidal neurons (8.96%) were light-responsive, that is, birthdated.
Red: pyramidal neurons (n = 7,411). ... Blue crosses: light-responsive pyramidal neurons (n = 664, 8.96%).
Extended Data Figure 2a
No unit is labelled light-responsive and no optogenetic pulse times are stored in the processed or raw files (stimulus and acquisition are empty in the processed files; a listing of every dataset in all 13 raw files finds only the ElectricalSeries, the LFP and the electrodes table). The paper's labels come from CellExplorer optoTag fields and pulses.events.mat files on the lab server, which the paper's data link reaches only through the lab databank and Globus, at no pinned identifier. The Methods say the pulses were given at the end of each session, in blocks of five 200 ms apart, and that the raw data were clipped out from 0.15 ms before to 0.8 ms after each pulse; they give no interval between blocks and do not say what the clipped samples hold. In the raw file of e16_3m2_211213 the wideband signal ends 2 s after the processed session, and ten 2 s windows over its last 30 min hold no flat or zeroed stretch on eight channels; if clipped samples are flat or zero, the stimulation period is not in the deposited recording. The other 10 wideband files (54 to 184 GB each) were not scanned.
BlockedFigure 1e· Data missing from the dataset
The fraction of light-responsive pyramidal cells per session follows a bell-shaped wave over birthdates, peaking at E15.5 (E13.5 5.39%, E14.5 11.16%, E15.5 14.74%, E16.5 9.16%; ANOVA p = 4e-4).
The fraction of light-responsive pyramidal neurons at each birthdate was consistent with the previously observed, bell-shaped wave of hippocampal neurogenesis peaking between E14 and E15 (Fig. 1e)
Figure 1e
What the paper reports
- ANOVA, F(3,92) = 8.525, p = 4 × 10⁻⁴ (n = 30, 24, 24 and 18 sessions)
Needs the light-responsive units of each session; see ed2-light-responsive-count.
BlockedFigure 1c· Data missing from the dataset
Neurons born on later days lie more superficially in the pyramidal layer (median normalized depth 0.71, 0.48, 0.28 and 0.19 for E13.5 to E16.5).
pyramidal neurons born on embryonic (E) days 13.5, 14.5, 15.5 and 16.5 occupied broadly overlapping, yet distinct, sublayers spanning the deep-to-superficial axis of the pyramidal layer (Fig. 1b,c)
Figure 1c
What the paper reports
- Kruskal–Wallis, H = 4.5 × 10^3, d.f. = 3, p = 0 (n = 2,657, 1,993, 7,749 and 9,173 tdTomato+ puncta)
Histology (tdTomato and DAPI images) is not in the dandiset and was not found elsewhere.
BlockedFigure 1f· Data missing from the dataset
Earlier-born light-responsive neurons more often shift their preferred theta phase in REM sleep (30.89% at E13.5 to 19.7% at E16.5; regression slope -3.42% per day).
received the strongest drive from the entorhinal cortex, as reflected indirectly by the largest fraction of pyramidal neurons with a theta-phase preference that shifted in rapid eye movement (REM) sleep (Fig. 1f)
Figure 1f
What the paper reports
- linear regression (bootstrap, one tailed), slope = −3.42%, p = 0.028 (n = 123, 106, 143 and 76 modulated neurons)
Needs light-responsive units by birthdate; see ed2-light-responsive-count. It also needs the LFP, which is in the raw files of only 12 sessions.
BlockedFigure 1g· Data missing from the dataset
Earlier-born light-responsive pyramidal neurons have higher firing rates (medians 1.57, 1.63, 1.62 and 1.16 Hz; Kruskal-Wallis p = 0.016).
Earlier born pyramidal neurons had higher firing rates (Fig. 1g)
Figure 1g
What the paper reports
- Kruskal–Wallis, H = 11.8186, d.f. = 3, p = 0.016 (n = 184, 132, 233 and 115 neurons)
Needs the light-responsive units; see ed2-light-responsive-count. Grouping all units by the mouse's birthdate would test a different quantity, as most units in a mouse are not birthdated.
BlockedFigure 1h· Data missing from the dataset
Burst index is an inverted-U function of birthdate (medians 0.1167, 0.1272, 0.136, 0.1082; Kruskal-Wallis p = 0.0044).
In contrast, the propensity to fire in bursts displayed an inverted-U function of birthdate (Fig. 1h).
Figure 1h
What the paper reports
- Kruskal–Wallis, H = 13.87, d.f. = 3, p = 0.0044 (n = 184, 132, 233 and 115 neurons)
Needs the light-responsive units; see ed2-light-responsive-count.
BlockedFigure 2a,b; Extended Data Figure 4· Data missing from the dataset
Same-birthdate (SBD) pairs fire more synchronously than different-birthdate (DBD) pairs in 11 of 13 animals.
Crosscorrelograms (CCGs) of spike trains recorded in the homecage pointed to greater synchrony between pairs of SBD than different-birthdate (DBD) pyramidal neurons (Fig. 2a), an observation that was prominent individually in 11 of 13 animals
Figure 2a,b; Extended Data Figure 4
SBD and DBD pairs cannot be formed without light-responsiveness labels; six of the homecage mice also have no units.
BlockedFigure 2c· Data missing from the dataset
SBD pairs cofire more than DBD pairs in theta cycles (median 0.0189 against 0.0087).
SBD pyramidal neurons exhibited greater pairwise correlations than DBD neurons in both individual theta cycles (Fig. 2c)
Figure 2c
What the paper reports
- two-sided Wilcoxon, p = 10⁻⁴⁵ (n = 3,751 SBD and 50,461 DBD pairs)
Needs SBD and DBD pairs (no labels) and theta cycles from the LFP (raw files of 12 sessions only).
BlockedFigure 2d· Data missing from the dataset
Intermediate-birthdate neurons have lower theta depth modulation in waking but not in REM sleep.
During theta oscillations, intermediate birthdate pyramidal neurons (E14.5 and E15.5) locked to a broader range of theta phases (that is, lower depth modulation) in the waking, but not the REM, state (Fig. 2d).
Figure 2d
What the paper reports
- wake, across birthdates: Kruskal–Wallis, H = 63.3868, d.f. = 3, p = 0 (n = 178, 127, 207 and 101 phase-locked neurons)
- REM sleep, across birthdates: Kruskal–Wallis, H = 3.077, d.f. = 3, p = 0.546 (n = 105, 99, 118 and 73 phase-locked neurons in REM sleep)
Needs light-responsive units by birthdate and the LFP.
BlockedFigure 2f· Data missing from the dataset
SPW-R firing rates and participation of light-responsive neurons are an inverted-U function of birthdate.
Sharp-wave ripple SPW-R-related firing rates and participation probability also exhibited an inverted-U-shaped relationship with birthdate (Fig. 2f).
Figure 2f
What the paper reports
- Kruskal–Wallis, H = 19.4058, d.f. = 3, p = 2 × 10⁻⁴ (n = 184, 132, 233 and 115 neurons, fraction of SPW-Rs with at least one spike)
Needs light-responsive units by birthdate; the ripples themselves are in the files.
BlockedFigure 2g· Data missing from the dataset
SBD pairs cofire more than DBD pairs in SPW-Rs (median 0.0399 against 0.0231).
SBD pyramidal neurons exhibited greater pairwise correlations than DBD neurons in both individual theta cycles (Fig. 2c) and SPW-Rs (Fig. 2e,g)
Figure 2g
What the paper reports
- two-sided Wilcoxon, p = 4 × 10⁻¹¹⁶ (n = 3,751 SBD and 50,461 DBD pairs)
Needs SBD and DBD pairs; no labels.
BlockedFigure 3c· Data missing from the dataset
Assembly members cofire more in SPW-Rs than member-nonmember pairs, and segregation from nonmembers depends nonlinearly on the members' birthdate.
Pairs of assembly members cofired in SPW-Rs more prominently than pairs of assembly non-members (Fig. 3c). Similar to the single-cell firing features, assembly member cofiring with assembly nonmembers depended nonlinearly on birthdate.
Figure 3c
What the paper reports
- members of the same assembly against member-nonmember pairs: two-sided Wilcoxon, p = 0 (n = 4,676 and 199,139 pairs)
- member-nonmember cofiring across member birthdates: ANOVA, F(3,199,135) = 717.4478, p = 0 (n = 105,357, 12,398, 37,946 and 43,438 pairs)
The member-nonmember part could be computed, but the analysis keeps only assemblies with a light-responsive member and groups them by birthdate, which needs the labels.
BlockedFigure 3e· Data missing from the dataset
Assemblies with intermediate-birthdate members are expressed in SPW-Rs at higher rates (E13.5 8.16, E14.5 9.25, E15.5 8.16, E16.5 6.9 Hz; ANOVA p = 0.0158).
Assemblies were expressed in SPW-Rs at rates that depended nonlinearly on assembly member birthdate (Fig. 3e).
Figure 3e
What the paper reports
- ANOVA, F(3,467) = 4.05, p = 0.0158 (n = 167, 67, 140 and 97 assemblies)
Assemblies are grouped by the birthdate of light-responsive members; no labels.
BlockedFigure 4c,d; Extended Data Figure 9· Data missing from the dataset
A model with a bell-shaped rate of neurogenesis and correlations among SBD neurons reproduces the assembly expression rates, and a uniform-neurogenesis model does not.
as we increased the strength of correlations, the bell-shaped model generated assembly dynamics yielding a good match to those observed in data (Fig. 4c,d and Extended Data Fig. 8d,e). ... which failed to capture assembly dynamics observed in data across all tested parameters (Extended Data Fig. 9).
Figure 4c,d; Extended Data Figure 9
The model is fitted to the assembly expression rates of fig3e-assembly-expression, which is blocked.
BlockedFigure 5b· Data missing from the dataset
Spatial information and coverage on the maze are largest in intermediate-birthdate neurons.
the spatial information content of spikes (measured in bits per second and as the number of spatial bins with reliably high firing rate) was largest in pyramidal neurons with intermediate birthdates (E14.5 and E15.5; Fig. 5b).
Figure 5b
What the paper reports
- spatial coverage across birthdates: Kruskal–Wallis, H = 13.99, d.f. = 3, p = 0.0062 (n = 164, 76, 111 and 115 neurons)
- spatial information across birthdates: Kruskal–Wallis, H = 20.23, d.f. = 3, p = 6 × 10⁻⁴ (n = 164, 76, 111 and 115 neurons)
Needs light-responsive units by birthdate.
BlockedFigure 5c· Data missing from the dataset
SBD pairs have higher spatial ratemap correlations than DBD pairs on the familiar maze (median 0.0152 against -0.0256).
SBD neurons exhibited greater overlap in spatial tuning, as reflected by higher spatial ratemap correlations compared with DBD neurons (Fig. 5c and Extended Data Fig. 5e,j).
Figure 5c
What the paper reports
- two-sided Wilcoxon, p = 1.9 × 10⁻¹⁰ (n = 2,609 SBD and 39,965 DBD pairs)
Needs SBD and DBD pairs; no labels.
BlockedFigure 5d· Data missing from the dataset
The ratemap overlap of SBD pairs depends on their anatomical distance, larger within 250 micrometres.
the strength of spatial ratemap correlations depended on the anatomical distance between SBD neurons, in that spatial ratemaps of SBD pyramidal neurons ≤250 μm apart exhibited systematically larger overlap than those of DBD neurons
Figure 5d
Needs SBD pairs and the shank of each unit; units have no electrode link and their group_id does not match the electrode groups in 64 of 65 files.
BlockedFigure 5f· Data missing from the dataset
Between left and right trials, ratemaps of SBD pairs reorganize closer together than those of DBD pairs.
Despite the different contexts between the two trial types, spatial ratemaps of SBD neurons tended to systematically reorganize closer together compared with those of DBD neurons (Fig. 5f).
Figure 5f
What the paper reports
- two-way ANOVA, main effect of common birthdate, F(1,81,197) = 37.93, p = 0 (n = 5,137 SBD and 77,398 DBD pairs)
Needs SBD and DBD pairs; no labels.
BlockedFigure 6e· Data missing from the dataset
In novel environments SBD pairs have higher ratemap correlations than DBD pairs (median 0.117 against 0.046).
As in the familiar environment (Fig. 5c), SBD neurons exhibited higher spatial ratemap correlations compared with DBD neurons (Fig. 6e).
Figure 6e
What the paper reports
- two-sided Wilcoxon, p = 4.8 × 10⁻⁹ (n = 1,510 SBD and 40,481 DBD pairs)
Needs SBD and DBD pairs; no labels.
BlockedFigure 6f· Data missing from the dataset
Ratemaps of SBD pairs remain closer together than those of DBD pairs between the familiar and novel environments.
Importantly, novel environment-related spatial ratemaps of SBD neurons tended to reorganize closer together compared with those of DBD neurons (Fig. 6a,b,f)
Figure 6f
What the paper reports
- two-way ANOVA, main effect of common birthdate, F(1,41,175) = 32.08, p = 0 (n = 2,404 SBD and 59,730 DBD pairs)
Needs SBD and DBD pairs; no labels.
BlockedFigure 7b· Data missing from the dataset
SBD pyramidal pairs converge onto the same interneurons more than DBD pairs (median convergence 0.2727 against 0.2).
SBD pyramidal neuron pairs converged on to postsynaptic interneurons more strongly than DBD pairs (Fig. 7b).
Figure 7b
What the paper reports
- two-sided Wilcoxon, p = 2.6 × 10⁻⁹⁷ (n = 3,751 SBD and 50,461 DBD pairs)
Needs SBD pairs and putative interneurons; neither labels nor cell types are in the files.
BlockedFigure 7c-e· Data missing from the dataset
Convergence onto interneurons and spike transmission probability are bell-shaped functions of the presynaptic neurons' birthdate.
both pyramidal cell-to-interneuron convergence and the strength of effective synaptic coupling (spike transmission probability) showed a bell-shaped relationship with birthdate (Fig. 7c–e).
Figure 7c-e
What the paper reports
- convergence on to interneurons across birthdates: Kruskal–Wallis, H = 58.4513, d.f. = 3, p = 0 (n = 1,200, 533, 1,579 and 439 pairs)
- spike transmission probability across birthdates: Kruskal–Wallis, H = 29.8231, d.f. = 3, p = 0 (n = 1,180, 440, 1,155 and 557 pairs)
Needs light-responsive units by birthdate and putative interneurons.
BlockedFigure 7f,g· Methods underspecified
Of all pyramidal pairs, 65.27% share at least one postsynaptic interneuron, and cofiring in SPW-Rs, theta cycles and ratemap overlap all increase with convergence.
Pairs of pyramidal cells with at least one shared postsynaptic interneuron (65.27% of all pairs) displayed a skewed convergence distribution (Fig. 7f) and all metrics of cofiring ... exhibited a positive linear relationship with the degree of pyramidal to interneuron convergence (Fig. 7g).
Figure 7f,g
What the paper reports
- cofiring in SPW-Rs across convergence quintiles: linear regression (bootstrap, two tailed), slope = 0.0032, tStat = 13.035, p = 0.001
- cofiring in theta cycles across convergence quintiles: linear regression (bootstrap, two tailed), slope = 0.0023, tStat = 7.15, p = 0.006
- spatial ratemap overlap across convergence quintiles: linear regression (bootstrap, two tailed), slope = 0.0049, tStat = 5.11, p = 0.005
Uses all pyramidal-interneuron pairs and needs no birthdate labels. The notebook applies the rate rule (units above 5 Hz as interneurons, 1,001 in all against the paper's 2,060) and the connection test of the Methods (0.8 ms CCG bins, hollowed-Gaussian baseline of 15 ms s.d., alpha 0.001) to two sessions. In e15_13f1_220117, whose mouse is not among the 15 of Figure 7f, the test at fixed lags of 0.8 to 3.2 ms detects connections in 5,073 of 11,319 possible pairs (0.448, against 31,932 of 184,230 or 0.173 in the paper), and 96.7% of pyramidal pairs share a target (paper 65.27%). In e13_26m1_211019, inside the Figure 7f cohort, it detects 0.407, with 96.7% of pairs sharing a target. The Methods test the three bins around the CCG peak, where this test uses fixed lags; a peak-centred variant (peak sought at lags up to 4.0 ms, a range the Methods do not give, chosen after the fixed-lag results were seen) detects 0.405 and 0.394, with 95.7% and 93.4% of pairs sharing a target. With a connection rate this far from the paper's under both forms, the procedure differs from the paper's, whose connections come from the lab's CellExplorer mono_res files (not public; the paper's code reads them and does not compute them). The difference may lie in this implementation as well as in what the Methods leave unstated (lag range, hollow fraction, CCG window). Of the paper's 96 sessions (the files without e15_13f1 and e16_3m2), 39 have no units in the dandiset, and cofiring in theta cycles needs the LFP, which the processed files lack.

Findings about the data

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

Data missingNo unit is labelled light-responsive (birthdated), and no optogenetic pulse times are stored in the processed or the raw files, so the paper's comparisons of same- and different-birthdate neurons and its birthdate profiles (22 of the 35 claims listed here) cannot be tested. The labels exist in the lab's CellExplorer files (optoTag, putativeCellType), which are not public at a pinned identifier.
Description missingUnits carry no putative cell type and no waveforms, though the paper classifies 7,411 pyramidal cells and 2,060 interneurons.
Data missingSix of the 17 mice (e13_1f1, e13_1m1, e14_1m1, e15_4m1, e15_4m2, e15_5m1; 39 files) have sleep states and ripples but no units and no position. The dandiset holds 8,201 units where the paper reports 9,471.
Data missingOf the 16 novel environment explorations, only 9 have position and trials, and no open field has position. The novel-cohort sessions hold 7 further epochs of 10 to 50 min without position or video that may be the missing explorations.
Metadata errorThe subject sex differs between files of the same mouse. e13_1f1 is Female in 3 files and Male in 2; e13_1m1 is Male in 9 and Female in 3. The value in most of each mouse's files gives the paper's 12 males and 5 females.
Metadata errorThe trials column is_familiar_maze is True only for the first two trials of sessions with a single maze recording, where every trial is on the familiar maze (112 True, 1,182 False).
Metadata errorIn several novel recordings (e13_26m1 211019, 211116, 211119; e15_13f1 220120; e16_3m2 211213) x and y lie between 0 and 1 though stated in cm.
Metadata errorTwelve of the 13 raw files give a session start of 2011-08-18 for sessions recorded in 2021 and 2022.
Metadata errorThe processed file of e16_3m1_210201 holds a copy of the 1250 Hz LFP of the raw file, labelled with a rate of 30,000 Hz and a conversion factor of 3.05e-13 V.
Identifier missingUnits have no link to the electrodes table, and their group_id values ("Group3") do not match the electrode group names ("Group 3") in 64 of 65 files, so a unit's shank and position on the probe cannot be recovered.
Description missingThe embryonic day of electroporation, the variable the paper is about, is stored only as the prefix of each subject id (e13 for E13.5); the age is given as P3M/P6M for every mouse.
OtherTwo files of e13_1f1 (200305, 200307) hold a single Awake interval for the whole session, so sleep was not scored, though both hold ripples.
OtherOnly 38 of 65 familiar-maze sessions have ten or more trials on each visited arm, and 6 have fewer than 20 trials, where the Methods require ten per arm in every session; 19 of 1,942 trials have no start or stop time.
Paper inconsistentThe Methods give 92 sessions, while Figure 1e (30, 24, 24 and 18 sessions) and Figure 7f give 96. The dandiset's files of the 15 homecage mice are 96 sessions that match Figure 1e by birthdate and the Methods' duration bounds exactly (113.7 to 475.6 min).
Paper inconsistentThe paper calls the novel-environment cohort of three mice separate, but one of them (e13_26m1) is also among the nine figure-eight mice, in the dandiset and in the paper's code.

Notebooks

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

Reproduction Birthdated CA1 pyramidal neurons in freely moving mice (Huszar et al. 2022)

Tests the findings of Huszar, Zhang, Blockus and Buzsaki (2022) that can be tested on dandiset 000552, which holds sleep states, sharp-wave ripples, spike-sorted units and position from 17 mice electroporated at E13.5 to E16.5. It checks the description of the dataset and tests the findings on all pyramidal neurons on familiar and novel mazes (population-vector decorrelation, firing rates, spatial information and ratemap correlations). The units carry no light-responsiveness label and no optogenetic pulse times are stored, so the comparisons of same- and different-birthdate neurons are blocked. All files

Reproducing Huszar et al. (2022) from dandiset 000552
reproduce_huszar_2022.ipynbExecuted, with outputs · Source

Verification

Round 1
2026-10-17
Agreed with 34 of 35 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's full text (the PMC author manuscript). The verifier tested helper functions on synthetic inputs and queried the archive's asset metadata for the blocked claims. Its report gave its own outcome for each claim; it agreed with the record on 34 of 35 outcomes, gave reproduced for cohort-birthdates, and for fig7fg-convergence-cofiring agreed on blocked but disputed the reason. Problems B6 (dependent bins and pairs treated as independent, as in the paper), B8 (skaggs_information weights by unsmoothed occupancy and divides by smoothed occupancy) and B9 (mean_rates divides by an end time 1 to 5 s short of the last spike in 57 files) it marked as not affecting a conclusion; they were left as they are, since the first follows the paper, the second follows the Methods' map definition with the occupancy probability of Skaggs et al., and the third changes rates by under 0.1%.
- cohort-birthdates: the verifier’s outcome was “Reproduced”. 17 mice and the birthdate counts 4/3/6/4 match. The notebook's 13 M / 4 F comes from taking each mouse's first file. The sex field differs between files of the same mouse; e13_1f1 is Male in 2 files and Female in 3, e13_1m1 is Male in 9 and Female in 3 (cell 7, and the DANDI asset metadata it queried). Taking each mouse's majority gives 12 M / 5 F, which matches. Problem B2 (affects a conclusion) is the same point.
Round 2
2026-10-17Agreed with 35 of 35 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's full text (the PMC10807234 author manuscript). The verifier agreed with all 35 outcomes, and for fig7fg-convergence-cofiring accepted the block while calling two parts of its reasoning weak. It quoted five sentences the outputs do not support: the count of 31 sessions without units (39), the statement on stimulation channels in the raw files (1 of 13 listed), the assumption about clipped pulses in cell 16, a swapped column label in the fig6c output, and the reading of the T-maze as the novel figure-eight. Remaining points bearing on a conclusion were B4 (fig5e rate rule), the weak fig6d-rate test, fig7fg's single out-of-cohort session and detector, and B7 (raw files). The round-1 response on fig7fg also gave 31 sessions; it is left as recorded, and the notes are corrected.

Method differences

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

The criterion took sex from the subject metadata without saying how to combine files that disagree; the value in most of a mouse's files is used, chosen after the per-file values were seen (the first round of this attempt read the first file and gave 13 and 4).cohort-birthdates
Session duration is the end of the last sleep-state or ripple interval; in 57 files the last spike falls 1.2 to 5.2 s later.sessions-durations
The criterion named the sleep condition without saying which outcome its failure gives; with the count, median and range holding and the sleep condition failing in 2 of 104 files, the outcome is taken as partial.sessions-durations
The session count was judged under two readings (92 and 96), as the paper gives both.sessions-durations
Uses the ripples stored in the files; detection was not repeated.spwr-duration
The pyramidal fraction uses a firing-rate rule, as the files hold no cell type.unit-count
The paper calls the novel cohort separate; the reading that matches takes the overlap from the paper's code, recorded as an ambiguity.maze-cohort
Two readings of "trials along each arm" (visited and expected) were used; neither holds.maze-task
Putative pyramidal cells by session mean rate (at most 5 Hz), not by waveform and autocorrelogram; the files hold no cell type or waveforms.fig5e-pv-decorrelation
Speed from smoothed linearized position, not a Kalman filter.fig5e-pv-decorrelation
The rate is the firing rate while running at 5 cm/s or faster inside maze trials, in place of the rate in LFP theta cycles; the LFP is in the raw files of 8 of the 9 novel sessions but was not used.fig6c-theta-rate-preserved
Novel mazes are only those with position; the open fields are not in the data.fig6c-theta-rate-preserved
Putative pyramidal cells by firing rate.fig6c-theta-rate-preserved
All pairs of putative pyramidal cells, where the paper's pairs each include a light-responsive neuron (not identifiable in the files).fig6c-novel-ratemap-corr-higher
Novel mazes are only the T-maze and linear tracks with position; the paper's novel pairs also come from open fields with two-dimensional maps.fig6c-novel-ratemap-corr-higher
Skaggs information over left and right maps of the whole linearized track, with putative pyramidal cells by firing rate; no open fields.fig6d-info-lower-novel
Running rate in place of the rate in LFP theta cycles.fig6d-rate-lower-novel
Putative pyramidal cells by firing rate; no open fields.fig6d-rate-lower-novel

Provenance

Attempt record: 000552-huszar-2022-01
Paper: Preconfigured dynamics in the hippocampus are guided by embryonic birthdate and rate of neurogenesis
Date: 2026-10-17
Made by: An agent, run by CatalystNeuro
Dataset: DANDI:000552
Version: 0.230630.2304 (doi:10.48324/dandi.000552/0.230630.2304)
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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