Physiological Properties and Behavioral Correlates of Hippocampal Granule Cells and Mossy Cells (DANDI:000003)

Claims

From the paper Physiological Properties and Behavioral Correlates of Hippocampal Granule Cells and Mossy Cells

Reproducing Senzai and Buzsaki (2017) from dandiset 000003 29

Notebook reproduce_senzai_2017.ipynb

Not reproducedResults, Physiological properties of granule cells and mossy cells, paragraph 1; Figure 2A
CA3 pyramidal neurons are most active during wake and least active during REM.
CA3 pyramidal neurons were most active during wake and least active during REM
Results, Physiological properties of granule cells and mossy cells, paragraph 1; Figure 2A
What the paper reports
- across states: Kruskal-Wallis test, p < 10⁻⁴
- pairwise between states: Bonferroni post hoc test, p < 10⁻⁴, Bonferroni-corrected
CA3 pyramidal cells fire least in REM (0.287 Hz; adjusted P = 1.1e-15 against NREM and 5.4e-09 against wake), but the NREM median (0.459 Hz) is above the wake median (0.441 Hz awake, 0.433 Hz with quiet wake) and the two do not differ (adjusted P = 0.77 and 0.59). The REM part of the claim holds. With home-cage awake time as wake (a variant), the wake median is 0.412 Hz and NREM against wake gives adjusted P = 0.14; CA3 units fire at similar rates awake in the home cage and during behaviour (0.424 and 0.415 Hz).
How the test differed from the paper’s method
- The paper's CA3 units come from a separate classification (Figure S2); here the dandiset's `pyramidal cell` label is used.
Not reproducedResults, State-dependent changes in spike transmission probabilities, paragraph 1; Figure 4B
GC to MC spike transmission is lower during NREM sleep than during waking (n = 31, P < 0.005).
Granule cell to mossy cell and granule cell to interneuron comparisons showed reduced probability of spike transmission during NREM compared to wake
Results, State-dependent changes in spike transmission probabilities, paragraph 1; Figure 4B
What the paper reports
- Wilcoxon signed rank test, p < 0.005 (n = 31 GC-MC pairs)
For 65 detected pairs, median transmission 0.0125 from GC spikes in awake periods and 0.0108 in NREM, lower in NREM for 34 pairs; Wilcoxon P = 0.39. The pairs are the automatic detections (see monosyn-gc-to-mc), not the paper's 31. Without the 22 first-bin pairs NREM is lower in 24 of 43 (P = 0.27); in the 17 files that give the shank, in 20 of 39 (P = 0.86).
How the test differed from the paper’s method
- Uses the automatic pair detections in place of the paper's curated pairs.
Not reproducedResults, Spatial and memory properties of granule cells and mossy cells, paragraph 2; Figure 6D
Granule cells with stable place fields remap less than mossy cells (Kruskal-Wallis P = 0.034; post hoc GC against MC P = 0.028).
but granule cells showed less remapping compared to mossy cells
Results, Spatial and memory properties of granule cells and mossy cells, paragraph 2; Figure 6D
What the paper reports
- across the three types: Kruskal-Wallis test, p = 0.034
- GC against MC: Bonferroni post hoc test, p = 0.028, Bonferroni-corrected
The GC median index (0.128) is below the MC median (0.293) but neither test is significant (Kruskal-Wallis P = 0.306; GC against MC P = 0.114, 0.342 after Bonferroni). With the variant place-cell rule, GC against MC P = 0.0648.
How the test differed from the paper’s method
- The paper's post hoc test is not named; Bonferroni-corrected Mann-Whitney tests are used.
Partially reproducedResults, Identification of granule cells and mossy cells in extracellular recordings, paragraph 2; Figure 1F
The second-stage classification divided dentate excitatory neurons into 586 putative granule cells (GC) and 500 putative mossy cells (MC).
K-means clustering on the three sets of features reliably segregated excitatory neurons as putative granule cells (n = 586) and putative mossy cells (n = 500)
Results, Identification of granule cells and mossy cells in extracellular recordings, paragraph 2; Figure 1F
The files hold 609 GC (paper 586, within tolerance) and 568 MC (paper 500, outside the tolerance of 450 to 550), from all 16 mice, counting each of the 101 files once.
How the test differed from the paper’s method
- Counts come from the dandiset's labels; the paper's classification was not re-run on all files.
Partially reproducedFigure 1A; STAR Methods, Unit classification
Narrow-waveform interneurons have a trough-to-peak latency below 0.425 ms, and among wide-waveform units the excitatory cells have a burst index above the threshold separating them from wide-waveform interneurons.
Units with trough-to-peak latency < 0.425 ms were classified as narrow-waveform putative interneurons ... Wide-waveform units were grouped into putative excitatory cells (E cells, red; burst index>1.8) and wide-waveform putative interneurons
Figure 1A; STAR Methods, Unit classification
Under both burst thresholds (1.2 in the Methods, 1.8 in the Figure 1A legend), 98.2% of GC and MC are wide-waveform and bursty and 91.7% or 93.3% of wide-waveform interneurons are wide and not bursty, but 82.5% of narrow-waveform interneurons have a latency below 0.425 ms (40% to 100% by mouse), short of the 90% criterion. The labels pool dentate and CA3 interneurons; 92.7% are below 0.525 ms, the paper's CA3 threshold, and in the 17 files that give the shank 94.4% of the 71 narrow-waveform interneurons on shanks with GC or MC and no CA3 unit are below 0.425 ms (variants). The stored waveforms have their trough at 0.80 ms, so latencies above about 0.75 ms cannot be measured. On the wide-band signal of the 17 files, 64.7% (unfiltered) or 88.5% (300 Hz high-pass) of narrow-waveform interneurons are below 0.425 ms.
How the test differed from the paper’s method
- Latency measured on the mean of the first 200 stored waveforms (1.6 ms long, filtering not stated in the files); the paper used unfiltered waveforms.
- The Methods and the Figure 1A legend give different burst thresholds (1.2 and 1.8); both were tested.
Partially reproducedResults, Identification of granule cells and mossy cells in extracellular recordings, paragraph 1
Narrow-waveform interneurons fire faster than wide-waveform interneurons (medians 7.97 and 2.11 Hz; Kruskal-Wallis P < 0.00001).
The mean firing rates of narrow (median = 7.97 Hz) and wide-waveform (median = 2.11 Hz) interneurons were significantly different
Results, Identification of granule cells and mossy cells in extracellular recordings, paragraph 1
What the paper reports
- Kruskal-Wallis test, p < 10⁻⁵
Narrow-waveform interneurons fire faster than wide-waveform ones (Kruskal-Wallis P = 5.3e-17 over the recording span, 1.4e-15 in awake periods), but the medians are outside tolerance under both readings (5.96 and 2.57 Hz over the recording; 8.75 and 3.08 Hz awake). In the 17 files that give the shank, interneurons on shanks with GC or MC and no CA3 unit have medians of 8.56 and 2.29 Hz over the recording, both within tolerance (P = 3.7e-08); this variant does not decide the outcome.
How the test differed from the paper’s method
- The interneuron labels include CA3 interneurons, which the paper counts apart, and the files do not say which region an interneuron is in.
- The paper does not define the rate; two readings were tested.
Partially reproducedResults, Optogenetic validation of the physiology-based separation of granule cells and mossy cells, paragraph 1; Figure 1H; STAR Methods, Optogenetic tagging
In DRD2-Cre::Ai35 mice, 29 of 107 putative mossy cells were suppressed by green light, against none of 202 putative granule cells, 8 of 68 wide-waveform and none of 69 narrow-waveform interneurons.
29 out of 107 putative mossy cells were light responsive ... whereas only eight of 68 w-I interneurons and none of the putative granule cells (n = 202) or n-I interneurons (n = 69) were suppressed significantly by green light
Results, Optogenetic validation of the physiology-based separation of granule cells and mossy cells, paragraph 1; Figure 1H; STAR Methods, Optogenetic tagging
In 26 DRD2-Cre::Ai35 sessions with 20 ms pulses (4 mice), 68 of 106 MC (0.642) are suppressed by at least 20% with the baseline before the pulse and 71 (0.670) with the baseline later in the cycle, against 6 (0.030) and 13 (0.066) of 198 GC. Wide-waveform interneurons 20 of 88, narrow-waveform 14 of 132. The MC fraction is far above the paper's 29 of 107 and GC are not zero; MC exceed four times the GC fraction under both readings. At a 50% threshold the MC fraction is 0.066. Adding a one-sided Poisson test (P < 0.05) to the 20% rule keeps all 68 MC and 5 GC. The 37 units of the Figure 1H legend equal the 29 MC and 8 wide-waveform interneurons of the text.
How the test differed from the paper’s method
- The Methods do not define the baseline of the light-pulse histogram; two readings were tested.
- The fifth DRD2 mouse (YutaMouse45) has no 20 ms pulses and is not included.
Partially reproducedResults, Physiological properties of granule cells and mossy cells, paragraph 1; Figure 2A
Granule cells fire most during NREM sleep and at similar rates during wake and REM.
Granule cells had their highest firing rates during NREM sleep and similar rates during wake and REM
Results, Physiological properties of granule cells and mossy cells, paragraph 1; Figure 2A
What the paper reports
- Kruskal-Wallis, p < 10⁻⁴
GC fire most in NREM (median 0.391 Hz against 0.077 Hz awake and 0.198 Hz REM; adjusted P 1.3e-86 and 8.7e-31), but REM rates exceed wake rates (adjusted P = 1.4e-25 with awake periods, 6.3e-23 with quiet wake), so wake and REM are not similar by the paper's test. With home-cage awake time as wake (a variant), wake and REM still differ (adjusted P = 3.3e-24).
How the test differed from the paper’s method
- The post hoc test is taken as Bonferroni-corrected Mann-Whitney tests; the paper names Kruskal-Wallis only.
Partially reproducedResults, Physiological properties of granule cells and mossy cells, paragraph 2
Slow-firing neurons are more strongly coupled to gamma than fast-firing ones (GC r = -0.176, MC r = -0.184, P < 0.0001 for each).
Interestingly, slow firing neurons had stronger phase coupling to gamma waves than fast firing cells
Results, Physiological properties of granule cells and mossy cells, paragraph 2
What the paper reports
- granule cells: r = -0.176, p < 10⁻⁴
- mossy cells: r = -0.184, p < 10⁻⁴
Over all units with a gamma MRL, GC r = -0.177 (P = 3.6e-05, within tolerance) and MC r = -0.161 (P = 0.00013, just outside the tolerance and above P = 0.0001). Over modulated units, GC -0.397 and MC -0.253, both P below 0.0001 and outside tolerance.
How the test differed from the paper’s method
- The paper does not say which units or which rate the correlation uses; two unit sets were tested with the rate over the recording span.
Partially reproducedResults, Granule cell-mossy cell spike transmission, paragraph 1; Figure 3B and 3C
5.5% of granule cells monosynaptically excite mossy cells (32 pairs), whereas no mossy cell significantly excites a granule cell.
The spike transmission probability between excitatory neuron pairs determined that 5.5% of the granule cells monosynaptically excited mossy cells (n = 32 pairs), whereas no mossy cell significantly excited putative granule cells
Results, Granule cell-mossy cell spike transmission, paragraph 1; Figure 3B and 3C
Among 4713 GC-MC pairs the automatic test finds 65 GC to MC pairs and 8 MC to GC pairs. The fraction is 0.107 (pairs over GC), 0.0805 (GC with a target over GC) or 0.0138 (pairs over tested pairs), none within 0.0495 to 0.0605. GC to MC pairs outnumber MC to GC pairs 65 to 8. Stricter thresholds lower both counts (56 and 6 at the 99.99999th percentile). For 22 GC to MC pairs the largest bin is the first of the window (1.5 to 2 ms); without them 43 pairs remain (0.0706 of GC). Of the 8 MC to GC pairs, 6 are in YutaMouse33, 4 involve one GC (unit 3 of YutaMouse33-150224) that is also synchronous with each of those MC, and 5 are also detected as GC to MC pairs, which fits common input. In the 17 files that give the shank, 17 of 39 GC to MC pairs are on one shank.
How the test differed from the paper’s method
- The paper inspected and refined each detection by hand; the automatic test alone is used here.
- The fraction 5.5% can be read three ways; all are shown.
Partially reproducedResults, Granule cell-mossy cell spike transmission, paragraph 3
Synchronous co-activation within 1 ms is found in 23% of mossy cells and 9% of CA3 pyramidal cells, but in fewer than 0.2% of granule cell pairs.
Only <0.2% of granule cell pairs showed significant peaks at < 1 ms while 23% of mossy cells and 9% of CA3 pyramidal cells showed synchronous (< 1 ms) co-activation
Results, Granule cell-mossy cell spike transmission, paragraph 3
GC pairs 4 of 3155 (0.0013, within the claim). MC 0.0766 of pairs or 0.433 of cells; CA3 0.0120 of pairs or 0.102 of cells; none within the tolerance of 0.23 and 0.09. Read as cells, MC and CA3 exceed the GC pair fraction more than ten times. In the 17 files that give the shank no synchronous pair is on one shank (0 of 160 MC, 0 of 51 CA3), so leaving out same-shank pairs changes little (cells MC 0.494, CA3 0.267 there); 143 of 160 synchronous MC pairs are on neighbouring shanks. No synchronous pair shares more than 15% of the sparser unit's spikes within 0.5 ms (MC at most 5.8%), so none looks like one neuron sorted twice.
How the test differed from the paper’s method
- Automatic detections without the paper's manual refinement.
- Pairs recorded on one shank cannot be left out in 83 of 101 files, which do not give the shank; in the other 17 files none of the synchronous pairs is on one shank.
Partially reproducedResults, Spatial and memory properties of granule cells and mossy cells, paragraph 1; Figure 5B
On the circular T-maze, the fraction of active neurons (above 1 Hz) is higher in the central arm than in the side arms, for granule cells, mossy cells and CA3 pyramidal cells (Kruskal-Wallis P < 0.00001 for each).
The fraction of active neurons (> 1 Hz) was significantly higher in the central arm compared to the side arms
Results, Spatial and memory properties of granule cells and mossy cells, paragraph 1; Figure 5B
What the paper reports
- Kruskal-Wallis test, p < 10⁻⁵
The central-arm median fraction of active units is above the side-arm median for GC (0.020 against 0.018, P = 0.043), MC (0.314 against 0.272, P = 2.2e-06) and CA3 (0.214 against 0.189, P = 0.048); only MC reach P < 0.00001. The bin-wise test treats smoothed, neighbouring bins as independent; compared unit by unit (a variant) the central arm is more active for MC (P = 2.8e-05) but not for GC (higher in 17, lower in 31 of 253 units, P = 0.83) or CA3 (P = 0.21).
How the test differed from the paper’s method
- T-maze runs are taken from the start of the central arm to 10 cm before the reward port in trials without light; the paper uses the time from gate opening to arrival at the reward.
- The meaning of the linearised T-maze positions is inferred from the values and the maze dimensions.
Partially reproducedResults, Spatial and memory properties of granule cells and mossy cells, paragraph 1; Figure 5C and 5D
Few granule cells have two or more place fields on the T-maze (6.6%), against 57.8% of mossy cells and 36.1% of CA3 pyramidal cells (Kolmogorov-Smirnov P < 0.0001).
only a small fraction (6.6% of recorded cells) had two or more. In contrast, 57.8% of mossy cells and 36.1% of CA3 pyramidal neurons had two or more place fields
Results, Spatial and memory properties of granule cells and mossy cells, paragraph 1; Figure 5C and 5D
What the paper reports
- Kolmogorov-Smirnov test, p < 10⁻⁴
Of all units, 4.3% of GC (253), 63.7% of MC (303) and 43.1% of CA3 (341) have two or more fields; of units with a field, 24.4%, 78.1% and 66.8%. No reading puts all three in tolerance (MC misses by 0.001 under reading a). GC have the fewest fields (KS P = 3.2e-53 against MC). The units come from 7 mice; the paper reports 213, 225 and 249 units from 9 mice.
How the test differed from the paper’s method
- Fields are counted on a map of the central arm from all runs plus each side arm, smoothed per segment; the paper builds left and right choice maps without saying how fields are combined.
- The 'local maximum' of the field rule is taken iteratively from the highest unassigned bin.
Partially reproducedResults, Spatial and memory properties of granule cells and mossy cells, paragraph 2; Figure 6C
Only 36.7% of granule cells with place fields (11 of 30) remap, against 61.3% of mossy cells (68 of 111) and 55.6% of CA3 pyramidal cells (80 of 144).
only a minority of granule cells (36.7%, n = 11 out of n = 30 place cells) showed remapping, whereas the majority of both mossy cells (61.3%, n=68 out of n = 111 place cells) and CA3 pyramidal neurons (55.6%, n = 80 out of n = 144) did
Results, Spatial and memory properties of granule cells and mossy cells, paragraph 2; Figure 6C
11 of 27 GC (0.407), 65 of 116 MC (0.560) and 73 of 143 CA3 (0.510) place cells remap. MC and CA3 are within tolerance; GC is 0.003 above it. GC remap least at every threshold shown (0.1 to 0.3).
ReproducedResults, Identification of granule cells and mossy cells in extracellular recordings, paragraph 3; Figure 1E
The waveform of granule cells is narrower than that of mossy cells.
Overall, the waveform of granule cells was narrower
Results, Identification of granule cells and mossy cells in extracellular recordings, paragraph 3; Figure 1E
GC median trough-to-peak latency 0.710 ms against MC 0.740 ms (Mann-Whitney P = 2.3e-14). The stored waveforms have their trough at 0.80 ms of 1.6 ms, and 43% of GC and 67% of MC have their peak at the end, so the result partly reflects how often each type is cut off; among units with the peak inside the window GC are not narrower (0.660 against 0.645 ms, P = 0.057). On the wide-band signal of the 17 files (window to 2.4 ms), the unfiltered waveform the Methods use gives GC 0.755 against MC 0.840 ms (P = 0.017); after a 300 Hz high-pass they do not differ (0.710 against 0.720 ms, P = 0.4).
How the test differed from the paper’s method
- Measured as trough-to-peak latency on the stored waveforms, where the paper describes the waveform shape through a PCA of its second derivative.
ReproducedResults, Physiological properties of granule cells and mossy cells, paragraph 1; Figure 2A
Mossy cells are more active than granule cells during both waking and NREM sleep (Kruskal-Wallis P < 0.0001 for each).
Mossy cells were more active than granule cells during both waking and NREM sleep
Results, Physiological properties of granule cells and mossy cells, paragraph 1; Figure 2A
What the paper reports
- waking: Kruskal-Wallis test, p < 10⁻⁴
- NREM: Kruskal-Wallis test, p < 10⁻⁴
MC median 0.736 Hz against GC 0.077 Hz in awake periods (Kruskal-Wallis P = 1.8e-114), 0.727 against 0.083 Hz with quiet wake, and 0.913 against 0.391 Hz in NREM (P = 2e-29). With home-cage awake time as wake (a variant), 0.692 against 0.077 Hz (P = 8.1e-102).
How the test differed from the paper’s method
- Wake is read as the `awake` periods, or `awake` with `quiet`; the states table does not describe its labels.
ReproducedFigure 1D; Discussion, first paragraph
Granule cells increase their firing in NREM sleep compared with waking, while mossy cells fire at equivalent rates in the two states.
Granule cells had cell bodies located near the depth of DS2 reversal, had increased firing in NREM compared to waking ... In contrast, mossy cells ... had equivalent firing rates in NREM and waking
Figure 1D; Discussion, first paragraph
Median NREM to wake ratio 4.63 for GC and 1.11 for MC (Mann-Whitney P = 3.9e-141; 4.28 and 1.11 with quiet wake), and the GC ratio is above the MC ratio in every mouse with both. The part saying MC fire at equivalent rates does not fully hold, as MC NREM rates are slightly above wake rates (Wilcoxon P = 1.4e-06). With home-cage awake time, 4.56 and 1.10.
ReproducedResults, Physiological properties of granule cells and mossy cells, paragraph 2; Figure 2C
Granule cells are more strongly phase-modulated by theta oscillations than mossy cells and fire at later theta phases (Kruskal-Wallis P < 0.0001 for both).
Granule cells fired on earlier phases of gamma waves ... and later phases of theta oscillations ... Granule cells were more strongly phase-modulated by both gamma ... and theta
Results, Physiological properties of granule cells and mossy cells, paragraph 2; Figure 2C
What the paper reports
- theta phase: Kruskal-Wallis test, p < 10⁻⁴
- theta phase modulation: Kruskal-Wallis test, p < 10⁻⁴
Modulated units 483 GC and 532 MC. Theta MRL GC 0.422 against MC 0.339 (Kruskal-Wallis P = 1.5e-20); GC fire later (circular means 30.8 and 12.0 degrees from the peak; P = 1e-17 with phases on (-pi, pi], 0.82 on [0, 2 pi)). After subtracting the uniform-phase expectation for the spike count (GC have fewer spikes), GC are still higher, at P = 0.00056. The bias-corrected MRL comparison (P = 0.00056) does not reach the paper's P < 0.0001. In the 17 files where it can be checked the theta-reference channel has a positive DS2 (+459 to +786 uV), so it lies below the DS2 reversal.
How the test differed from the paper’s method
- Phases from the theta-reference channel the conversion flagged, during up to an hour of awake periods per file; the paper's periods and reference channel are not stated.
- Phase comparisons depend on where the cycle is cut; both cuts are shown and the claim holds on one.
ReproducedResults, Physiological properties of granule cells and mossy cells, paragraph 2; Figure 2B
Granule cells are more strongly phase-modulated by gamma oscillations than mossy cells and fire at earlier gamma phases (Kruskal-Wallis P < 0.0001 for both).
Granule cells fired on earlier phases of gamma waves ... Granule cells were more strongly phase-modulated by both gamma
Results, Physiological properties of granule cells and mossy cells, paragraph 2; Figure 2B
What the paper reports
- gamma phase: Kruskal-Wallis test, p < 10⁻⁴
- gamma phase modulation: Kruskal-Wallis test, p < 10⁻⁴
Modulated units 345 GC and 475 MC. Gamma MRL GC 0.319 against MC 0.212 (P = 4.8e-43; 0.219 against 0.166, P = 4.1e-18, after subtracting the uniform-phase expectation); GC fire earlier (circular means -20.2 and 1.7 degrees; P = 1.2e-23 on (-pi, pi], 0.18 on [0, 2 pi)).
How the test differed from the paper’s method
- As theta-modulation.
ReproducedResults, Physiological properties of granule cells and mossy cells, paragraph 2; Figure 2D and 2E
Granule cells are more effectively recruited by type 2 dentate spikes than mossy cells and fire earlier (Kruskal-Wallis P < 0.0001 for both).
Granule cells were also more effectively recruited to LFP DS2 than mossy cells ... and fired earlier
Results, Physiological properties of granule cells and mossy cells, paragraph 2; Figure 2D and 2E
What the paper reports
- DS2 peak firing ratio: Kruskal-Wallis test, p < 10⁻⁴
- DS2 firing peak timing: Kruskal-Wallis test, p < 10⁻⁴
Median DS2 peak ratio GC 6.88 against MC 4.82 (Kruskal-Wallis P = 1.1e-10); median peak time -3.0 against +1.0 ms (P = 2.2e-09). 10 GC and 14 MC dropped for a zero baseline.
How the test differed from the paper’s method
- The DS2 events are those stored in the files; the peak-ratio baseline (50 to 100 ms on both sides) is a choice, as the paper does not give it.
ReproducedResults, Granule cell-mossy cell spike transmission, paragraph 2; Figure 3E to 3G
Spike transmission probability from granule cells to mossy cells increases from the first to the second spike of a granule cell burst (P < 0.001).
Spike transmission probability increased from first to second spike
Results, Granule cell-mossy cell spike transmission, paragraph 2; Figure 3E to 3G
What the paper reports
- p < 0.001
For the 65 detected pairs, the median transmission probability is 0.0066 for first and 0.0334 for second burst spikes, higher in 58 pairs (Wilcoxon P = 1.2e-09); it holds with bursts at 4 ms (P = 4.4e-08) and 10 ms (P = 5.5e-10). The detected pairs are partly reproduced (see monosyn-gc-to-mc) and number 65 against the paper's 32. It also holds with only burst intervals of 3.5 to 6 ms, where the two response windows do not overlap (58 of 65, P = 7.6e-10), with a baseline hollowed by 60% (P = 1.2e-09), and without the 22 first-bin pairs (41 of 43, P = 3.8e-11). First spikes transmit less than single spikes (0.0066 against 0.0147), which the outputs do not explain.
How the test differed from the paper’s method
- Bursts are spikes at most 6 ms apart, a choice; the paper does not define them.
- Transmission is the excess over the plain Gaussian baseline of the Methods.
ReproducedResults, Spatial and memory properties of granule cells and mossy cells, paragraph 1; Figure 5E and 5F
Granule cells have the lowest within-field peak firing rates (GC against MC, Kolmogorov-Smirnov P < 0.003) and the lowest spatial information of the three types (P < 0.0005).
Of the three neuron types, granule cells had the lowest within-place field peak firing rates ... and lowest spatial information
Results, Spatial and memory properties of granule cells and mossy cells, paragraph 1; Figure 5E and 5F
What the paper reports
- within-field peak rate, GC against MC: Kolmogorov-Smirnov test, p < 0.003
- spatial information: Kolmogorov-Smirnov test, p < 5 × 10⁻⁴
Within-field peak GC 2.63 Hz against MC 5.68 Hz (KS P = 4.5e-05); spatial information GC 0.035 bits/s against MC 0.603 (P = 1.6e-49) and CA3 0.293 (P = 1.5e-29).
How the test differed from the paper’s method
- As tmaze-multiple-fields.
ReproducedResults, Spatial and memory properties of granule cells and mossy cells, paragraph 1
The fraction of splitter cells, whose central-arm firing predicts the coming turn, is comparable in granule cells, mossy cells and CA3 pyramidal cells.
The fraction of splitter cells was comparable in the three principal cell groups
Results, Spatial and memory properties of granule cells and mossy cells, paragraph 1
Splitters 0 of 17 GC, 4 of 179 MC and 4 of 141 CA3 with a central-arm field; chi-square P = 0.76. Fisher's exact test gives P = 1 for GC against MC and against CA3 and 0.73 for MC against CA3. Under equal fractions 0.40 GC splitters would be expected, so the GC comparison has almost no power.
How the test differed from the paper’s method
- The paper names no test for comparing the fractions; a chi-square test was fixed in the criterion.
ReproducedResults, Spatial and memory properties of granule cells and mossy cells, paragraph 2; Figure 6C and 6D
For neurons with stable place fields, the remapping index between open fields A and B is above zero in each group (Wilcoxon signed-rank; GC P < 0.05, MC and CA3 P < 0.00001).
For neurons with significant place fields ... the remapping index was significantly higher than zero in each group
Results, Spatial and memory properties of granule cells and mossy cells, paragraph 2; Figure 6C and 6D
What the paper reports
- GC: Wilcoxon signed rank test, p < 0.05
- MC: Wilcoxon signed rank test, p < 10⁻⁵
- CA3: Wilcoxon signed rank test, p < 10⁻⁵
Place cells GC 27, MC 116, CA3 145 (paper 30, 111, 144), of which 27, 116 and 143 have a remapping index; median remapping index 0.128 (P = 0.0013), 0.293 (P = 1.5e-13) and 0.207 (P = 8.6e-14). Units per type 246, 182 and 317 in 5 mice (paper 247, 181, 317 in 5 mice).
How the test differed from the paper’s method
- The place-field 'local maximum' is the map's peak; the speed is from positions smoothed over 0.25 s.
ReproducedResults, Spatial and memory properties of granule cells and mossy cells, paragraph 3; Figure 6E to 6G
Population-vector remapping is smaller for granule cells than for mossy cells and CA3 pyramidal cells, for populations of 5, 10, 15 and 20 place cells.
The magnitude of population remapping was significantly smaller for granule cells compared to mossy cells and CA3 pyramidal cells ... These results remained robust within a range of threshold values with different numbers of neurons comprising the population vector
Results, Spatial and memory properties of granule cells and mossy cells, paragraph 3; Figure 6E to 6G
What the paper reports
- 20 place cells, across types: Kruskal-Wallis test, p < 10⁻⁵
- 20 place cells, post hoc: Bonferroni post hoc, p < 10⁻⁵, Bonferroni-corrected
- 5, 10, 15 and 20 place cells, across types: Kruskal-Wallis test, p < 10⁻⁵
- 5, 10, 15 and 20 place cells, post hoc: Bonferroni post hoc, p < 0.05, Bonferroni-corrected
For 5, 10, 15 and 20 cells, the GC median index (0.162 to 0.210) is below the MC (0.253 to 0.302) and CA3 (0.251 to 0.352) medians, Kruskal-Wallis P from 5.8e-35 to 8.1e-190. 71% to 89% of GC draws fall below the MC median. These P values treat 1000 overlapping draws from the same 27 GC as independent and do not measure the evidence. With all place cells together the index is 0.22 for GC and 0.25 for MC, and permuting the GC and MC labels gives P = 0.32 for that difference.
How the test differed from the paper’s method
- Place cells pooled across sessions and mice for the draws; the paper does not say whether it pooled.
ReproducedResults, Transmission of place information between granule cells and mossy cells, paragraph 1; Figure 7A and 7B
Mossy cells rarely inherit place fields from single presynaptic granule cells; of 10 place fields of connected granule cells, only 2 overlapped a field of the postsynaptic mossy cell.
Across 10 place fields from granule cells and 48 place fields from mossy cells, only two place fields showed overlap between monosynaptically connected pairs
Results, Transmission of place information between granule cells and mossy cells, paragraph 1; Figure 7A and 7B
5 of 16 GC fields (0.31) of GC with a detected MC partner overlap a partner MC field, within the criterion of at most a third; 15 of 23 GC partners have no T-maze field (paper 11 of 18). The result is close to the criterion's limit and uses the automatic pair detections (see monosyn-gc-to-mc). With the partner replaced by a random other MC of the session (1000 draws), the overlap is 0.38 (5th to 95th percentile 0.19 to 0.62) and 33% of draws are at or below 0.31, so the overlap with the connected MC is at the chance level.
How the test differed from the paper’s method
- "Rarely" was fixed as at most a third of GC fields; the paper gives 2 of 10.
- Pairs are automatic detections, not the paper's curated pairs.
ReproducedResults, Transmission of place information between granule cells and mossy cells, paragraph 2; Figure 7J
In the open fields, the rate maps of connected granule cells and mossy cells are not correlated within the granule cell's place field (median near 0, n = 19, Wilcoxon P = 0.60).
GC-MC map correlations of all comparisons in which the presynaptic GC had significant place fields. Note median correlation around 0
Results, Transmission of place information between granule cells and mossy cells, paragraph 2; Figure 7J
What the paper reports
- Wilcoxon signed rank test, p = 0.6 (n = 19 comparisons)
18 comparisons from 6 pairs in 4 sessions; median r = -0.038, Wilcoxon P = 0.67; 5 of 18 above 0.5 (paper 2 of 19). The 18 comparisons come from only 6 pairs, so they are not independent.
How the test differed from the paper’s method
- Pairs are automatic detections; the open-field sessions include the curtain sessions, as the paper's five sessions per pair do.
ReproducedFigure 1G; Results, Identification of granule cells and mossy cells in extracellular recordings, paragraph 3
Mossy cells are located deeper than granule cells relative to the reversal of the type 2 dentate spike (DS2) (Mann-Whitney P < 0.001).
MC were located significantly deeper than GC
Figure 1G; Results, Identification of granule cells and mossy cells in extracellular recordings, paragraph 3
What the paper reports
- Mann-Whitney U-test, p < 0.001
In the 17 files with the wide-band signal and shanks (4 mice; 139 GC, 226 MC with at least 20 spikes in the wide-band window), the DS2 amplitude at the unit's site, read from the wide-band signal, has a median of +580 uV for MC and +232 uV for GC (Mann-Whitney P = 2e-40); 100% of MC (to two decimals) and 80% of GC sit where DS2 is positive, and MC are deeper in each of the 4 mice. With the site the electrodes table gives (a variant), +271 against -38 uV (P = 5.7e-09), with YutaMouse33 reversed; the two sites share the LFP column for 9% of units and the DS2 sign for 63%.
How the test differed from the paper’s method
- Depth is read from the DS2 amplitude at the site, as the files give no site coordinates; the paper measures distance from the DS2 reversal.
- 17 of 101 files only. The site is the wide-band column where the unit's spike is largest (300 Hz high-pass, about 150 s of signal per file), as the electrodes table's channel map disagrees with the wide-band signal; the criterion's shank channel taken through the table is shown as a variant.
- DS2 amplitude from about 220 s of LFP per file (the two LFP chunks with the most DS2 peaks).
ReproducedResults, Identification of granule cells and mossy cells in extracellular recordings, paragraph 2; Figure 1D to 1F; STAR Methods, Unit classification
K-means clustering on the DS2 amplitude at the unit's site, the NREM to wake rate ratio and two principal components of the waveform's second derivative separates excitatory dentate units into granule cells and mossy cells.
Based on the bimodality of the distribution, K-means clustering over the four parameters was performed to classify E units into putative GC (yellow) and MC (magenta)
Results, Identification of granule cells and mossy cells in extracellular recordings, paragraph 2; Figure 1D to 1F; STAR Methods, Unit classification
On 364 GC and MC of the 17 files (32 dropped for fewer than 20 spikes in the wide-band window, no DS2 site or a zero awake rate), k-means on the DS2 amplitude at the wide-band site, the Methods' NREM to wake ratio and two components of the second derivative of the unfiltered wide-band waveform agrees with the labels for 95.3% of units (93% to 97% by mouse). Without the DS2 amplitude 89.0%, without the first waveform component 88.5%, without the ratio 94.2%. With the log ratio 95.6%, with home-cage awake time 94.8%, with the stored waveforms and the table's site 92.8%.
How the test differed from the paper’s method
- Run on 17 of 101 files (364 of 1177 GC and MC); the paper ran it on all excitatory units.
- The site and the waveform are read from the wide-band signal (about 150 s per file), as the electrodes table's channel map disagrees with it; the stored waveforms with the table's site are a variant.
- Wake is the `awake` periods, as fixed in the criterion; the Methods name awake time in the home cage, shown as a variant.
- The four features are standardised and clustered directly; the paper took a second PCA before k-means, which does not change k-means on all components.
- The second-derivative window starts at the trough; the Methods say 0 to 0.8 ms without naming the origin.

Not tested in a notebook 2

2 metadata insufficient

BlockedResults, Granule cell-mossy cell spike transmission, paragraph 1; Figure 3D· Metadata insufficient
Granule cells reside 59 +- 35 um above the mossy cells they drive.
Granule cells resided 59±35 μm above their driven mossy cell partners
Results, Granule cell-mossy cell spike transmission, paragraph 1; Figure 3D
Needs the positions of the recording sites in um. The electrodes tables give x, y and z as NaN in every file, the order of sites along a shank is not stated, and 83 of 101 files do not say which shank a unit was on. The paper's own monosynaptic pairs were not converted either. The Methods give 8 sites per shank on the 8-shank probes and 10 on the 6-shank probes, staggered with 20 um vertical separation, but the table's site numbers do not follow depth (the DS2 profile along them crosses zero more than once on 43 of 64 shanks with a crossing), and a unit's largest wide-band column lies on the shank the table gives for only 45% of units. In the 17 files that give the shank, the order of each shank's stored waveform channels can be recovered from the units' spikes in the wide-band signal, and along it the DS2 profile crosses zero once on 43 of the 51 shanks that cross, so it is consistent with depth. This attempt wrote no criterion for the claim and ran no test on that order; a new attempt could test it on these 17 files (39 detected GC to MC pairs).
BlockedResults, Identification of granule cells and mossy cells in extracellular recordings, paragraph 3; Figure S3D to S3F· Metadata insufficient
Granule cell spikes show a delay from the soma to the proximal dendrites, absent in mossy cells.
Indeed, the spikes of granule cells showed a delay from the soma to the proximal dendrites ... whereas no such delays were observed in putative mossy cells
Results, Identification of granule cells and mossy cells in extracellular recordings, paragraph 3; Figure S3D to S3F
Needs each unit's waveform along the shank with the sites' vertical positions; the files give no site coordinates (x, y, z are NaN) and the stored waveforms span 1.6 ms at the channels of the shank without their positions. In 83 files the shank itself is not given. The wide-band signal gives each unit's spike on every column, and in those 17 files the order of each shank's stored channels, recovered from the units' spikes, is consistent with depth (see gc-mc-distance). This attempt wrote no criterion for the claim and ran no test of a delay along that order; a new attempt could.

Findings about the data

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

File format errorIn 24 files the end index of the first unit in the units table is short by a multiple of 65,536 spikes (k = 1 to 7). The missing spikes open the second unit's spike train, which then restarts at the beginning of the recording, so the second unit's times are not sorted. The first moved spike follows the first unit's last stored spike by 2 ms to 0.5 s. This looks like an integer overflow at conversion; the waveforms follow the same boundaries.
Metadata errorThe genotypes in the files (6 SST-Cre, 5 Drd2-Cre::Ai35, 4 POMC-Cre::Arch, 1 POMC-Cre::Ai35) do not match the paper's 16 mice (7 SST-Cre, 5 DRD2-Cre::Ai35, 3 POMC-Cre::Ai35 and 1 wild type).
Description missing83 of 101 files do not say which shank each unit was recorded on (`shank_id` is a cluster number, and there is no `electrode_group`), and no file gives site coordinates (x, y, z are NaN). The paper's depth measures can be computed for 17 files only, and distances between cells not at all.
Description missingThe T-maze position series (`twhl_linearized`, `twhl_norm`) are not described. The values show column 0 of `twhl_linearized` runs along the central arm (0 to 2) and column 1 is an angle along the circular side arms, negative for the left arm, which fits the maze in the Methods but is not stated.
Description missingThe states table holds `awake`, `quiet`, `nrem`, `rem` and `transit` without a description; the paper names wake, NREM and REM, and whether `quiet` counts as wake is not stated.
Description missingThe interneuron labels (narrow-waveform, wide-waveform) do not say whether the unit is in the dentate gyrus or CA3, which the paper separates; only the excitatory label was split by region (granule cell or CA3 pyramidal cell).
Data missingThe monosynaptic connections the authors detected and curated (`MonoSynConvClick.mat`) were not converted (the conversion code comments them out), so the pair-based results (Figures 3, 4 and 7) cannot be checked on the authors' pairs.
OtherThe dandiset holds 568 mossy cells and 609 granule cells against the paper's 500 and 586, and 237 units labelled `missing` (units of the spike sorting with no row in the authors' unit summary).
File format errorThe light-pulse series PulseStim_5V_20ms_LD12 of YutaMouse57-161006 holds 89,086 times of which 24,286 are duplicates, and its times decrease once.
OtherThe units table has two layouts. 18 files (mice 33, 41, 42 and 54) carry an `electrode_group` column naming each unit's shank, one of them without waveforms (YutaMouse33-150218, which the conversion script lists as excluded); the other 83 files do not.
Description missingSeven dates hold two files of one mouse (the second named with `b`). They share no spike trains, so they are different recordings, but the metadata do not say whether they come from a second probe or a second session.
Paper inconsistentThe Methods give a burst index threshold of 1.2 for excitatory cells, and the Figure 1A legend gives 1.8.
Metadata errorIn the 17 files with the wide-band signal and each unit's shank, the electrodes table's assignment of columns to shanks and sites disagrees with the data. The column where a unit's spike is largest in the wide-band signal lies on the shank the units table gives for 45% of units (11% to 79% by file) and is the table's own site for 9%, and the DS2 amplitude along the table's site numbers crosses zero more than once on 43 of 64 shanks where it crosses at all. The wide-band and LFP columns match each other. The units' shanks (`electrode_group`) and stored waveform channels fit the wide-band signal under one fixed map of columns, the same in all 4 mice (a map from three mice gives the column of a unit's largest spike for 78% to 89% of units in the fourth, against 5% to 13% for the table), so the error is in the table, whose blocks of 8 rows do not match the probe's columns.
Description missingThe stored spike waveforms are about 5 times larger than the same spikes in the wide-band signal (median peak-to-peak 421 against 81 uV, 300 Hz high-pass), and their filtering and scaling are not described. They match the wide-band spike best after a 300 Hz high-pass (median correlation 0.987, against 0.981 unfiltered and 0.867 at 800 Hz), with a gain of 5.08, close to 5.13, the inverse of the wide-band conversion of 0.195 uV per count, which is consistent with waveforms stored in ADC counts and read as microvolts. Each holds 1.6 ms with the trough at 0.8 ms, which cuts off the peak of 43% of GC, 67% of MC and 78% of CA3 waveforms.

Notebooks

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

Reproduction Granule cells and mossy cells of the dentate gyrus (Senzai and Buzsaki 2017)

Tests the findings of Senzai and Buzsaki (2017) on dandiset 000003, which holds silicon probe recordings of the dentate gyrus and CA3 in 16 mice, in 101 files from 94 recording days, with labelled granule cells, mossy cells, CA3 pyramidal cells and interneurons, sleep states, dentate spikes, light pulses, and positions on a circular T-maze and in open fields. It covers firing by brain state, theta and gamma phase locking, recruitment by dentate spikes, optogenetic tagging, monosynaptic transmission, place fields and remapping, and, on the 17 files that give each unit's shank, depth and the classification of granule and mossy cells. All files

Reproducing Senzai and Buzsaki (2017) from dandiset 000003
reproduce_senzai_2017.ipynbExecuted, with outputs · Source

Verification

Round 1
2026-10-16Agreed with 31 of 31 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. The verifier queried the archive metadata and tested helper functions on synthetic inputs. Its report had no attempt record and gave its own outcome for each claim; all 31 agree with the record.
Round 2
2026-10-16Agreed with 31 of 31 outcomes. Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook). Reviewed: Round 2. The full executed notebook of the first revision, the helper module, the claims file and the attempt record, with the paper. The verifier agreed with all 31 outcomes. It also flagged that cell 0 ('The raw wide-band signal is in 17 files and is not used') and cell 5 ('(not used)') are stale, as cells 21, 24, 29, 35, 107 and 110 use the wide-band signal; both were corrected.

Method differences

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

Counts come from the dandiset's labels; the paper's classification was not re-run on all files.unit-counts
Latency measured on the mean of the first 200 stored waveforms (1.6 ms long, filtering not stated in the files); the paper used unfiltered waveforms.first-stage-labels
The Methods and the Figure 1A legend give different burst thresholds (1.2 and 1.8); both were tested.first-stage-labels
The interneuron labels include CA3 interneurons, which the paper counts apart, and the files do not say which region an interneuron is in.interneuron-rates
The paper does not define the rate; two readings were tested.interneuron-rates
Measured as trough-to-peak latency on the stored waveforms, where the paper describes the waveform shape through a PCA of its second derivative.gc-narrower-waveform
The Methods do not define the baseline of the light-pulse histogram; two readings were tested.optotag-drd2
The fifth DRD2 mouse (YutaMouse45) has no 20 ms pulses and is not included.optotag-drd2
Wake is read as the `awake` periods, or `awake` with `quiet`; the states table does not describe its labels.mc-more-active
The post hoc test is taken as Bonferroni-corrected Mann-Whitney tests; the paper names Kruskal-Wallis only.gc-nrem-highest
The paper's CA3 units come from a separate classification (Figure S2); here the dandiset's `pyramidal cell` label is used.ca3-wake-highest
Phases from the theta-reference channel the conversion flagged, during up to an hour of awake periods per file; the paper's periods and reference channel are not stated.theta-modulation
Phase comparisons depend on where the cycle is cut; both cuts are shown and the claim holds on one.theta-modulation
As theta-modulation.gamma-modulation
The paper does not say which units or which rate the correlation uses; two unit sets were tested with the rate over the recording span.gamma-rate-correlation
The DS2 events are those stored in the files; the peak-ratio baseline (50 to 100 ms on both sides) is a choice, as the paper does not give it.ds2-recruitment
The paper inspected and refined each detection by hand; the automatic test alone is used here.monosyn-gc-to-mc
The fraction 5.5% can be read three ways; all are shown.monosyn-gc-to-mc
Bursts are spikes at most 6 ms apart, a choice; the paper does not define them.burst-facilitation
Transmission is the excess over the plain Gaussian baseline of the Methods.burst-facilitation
Uses the automatic pair detections in place of the paper's curated pairs.state-transmission
Automatic detections without the paper's manual refinement.zero-lag-synchrony
Pairs recorded on one shank cannot be left out in 83 of 101 files, which do not give the shank; in the other 17 files none of the synchronous pairs is on one shank.zero-lag-synchrony
T-maze runs are taken from the start of the central arm to 10 cm before the reward port in trials without light; the paper uses the time from gate opening to arrival at the reward.tmaze-central-active
The meaning of the linearised T-maze positions is inferred from the values and the maze dimensions.tmaze-central-active
Fields are counted on a map of the central arm from all runs plus each side arm, smoothed per segment; the paper builds left and right choice maps without saying how fields are combined.tmaze-multiple-fields
The 'local maximum' of the field rule is taken iteratively from the highest unassigned bin.tmaze-multiple-fields
As tmaze-multiple-fields.tmaze-peak-info
The paper names no test for comparing the fractions; a chi-square test was fixed in the criterion.tmaze-splitters
The place-field 'local maximum' is the map's peak; the speed is from positions smoothed over 0.25 s.remap-positive
The paper's post hoc test is not named; Bonferroni-corrected Mann-Whitney tests are used.remap-gc-lt-mc
Place cells pooled across sessions and mice for the draws; the paper does not say whether it pooled.pv-remap
"Rarely" was fixed as at most a third of GC fields; the paper gives 2 of 10.inheritance-tmaze
Pairs are automatic detections, not the paper's curated pairs.inheritance-tmaze
Pairs are automatic detections; the open-field sessions include the curtain sessions, as the paper's five sessions per pair do.inheritance-openfield
Depth is read from the DS2 amplitude at the site, as the files give no site coordinates; the paper measures distance from the DS2 reversal.mc-deeper
17 of 101 files only. The site is the wide-band column where the unit's spike is largest (300 Hz high-pass, about 150 s of signal per file), as the electrodes table's channel map disagrees with the wide-band signal; the criterion's shank channel taken through the table is shown as a variant.mc-deeper
DS2 amplitude from about 220 s of LFP per file (the two LFP chunks with the most DS2 peaks).mc-deeper
Run on 17 of 101 files (364 of 1177 GC and MC); the paper ran it on all excitatory units.gc-mc-classification
The site and the waveform are read from the wide-band signal (about 150 s per file), as the electrodes table's channel map disagrees with it; the stored waveforms with the table's site are a variant.gc-mc-classification
Wake is the `awake` periods, as fixed in the criterion; the Methods name awake time in the home cage, shown as a variant.gc-mc-classification
The four features are standardised and clustered directly; the paper took a second PCA before k-means, which does not change k-means on all components.gc-mc-classification
The second-derivative window starts at the trough; the Methods say 0 to 0.8 ms without naming the origin.gc-mc-classification

Provenance

Attempt record: 000003-senzai-2017-01
Paper: Physiological Properties and Behavioral Correlates of Hippocampal Granule Cells and Mossy Cells
Date: 2026-10-16
Made by: An agent, run by CatalystNeuro
Dataset: DANDI:000003
Version: 0.260218.2052 (doi:10.48324/dandi.000003/0.260218.2052)
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.

DANDI:000004 →