001754-knierim-2000-01 (earlier attempt) · Three-dimensional spatial selectivity of hippocampal neurons during space flight (DANDI:001754)

Claims

From the paper Three-dimensional spatial selectivity of hippocampal neurons during space flight

Deprecated: Its claims were written from the abstract and figure titles only. Read against the full text on 2026-10-20, flight-spatial-code was judged with a shuffle test the paper does not use (the paper compares spatial information with preflight), and four dropped claims are stated in the paper. Its outcomes are shown but not counted.

Reproducing Knierim et al. (2000) from dandiset 001754 2

Notebook reproduce_knierim_2000.ipynb

Not reproducedMain text, paragraph beginning "During the Neurolab Space Shuttle mission", last sentence; supported by the paragraphs beginning "Spatial firing patterns of 16 active place cells" and "The mean spatial-information content for all 7" and Figures 2a, 2c and 3a; also the standfirstverifier disagreed at first
In flight, after an initial period, hippocampal place cells on the Escher staircase showed normal, spatially specific firing, with spatial information per spike not different from the same rats' preflight cells.
Nonetheless, place cells eventually demonstrated normal, spatially specific firing properties.
Main text, paragraph beginning "During the Neurolab Space Shuttle mission", last sentence; supported by the paragraphs beginning "Spatial firing patterns of 16 active place cells" and "The mean spatial-information content for all 7" and Figures 2a, 2c and 3a; also the standfirst
The third verification round agreed with the change from partially_reproduced to not_reproduced. On flight day 9, 12 of 25 Rat1 units (0.48) have spatial information above the 95th percentile of 500 circular-shift shuffles on the Escher staircase (binomial p = 6.9e-10 against 0.05), and 3 of 28 Rat2 units (0.107, p = 0.16). By the criterion Rat1 is above chance but below 0.5 and Rat2 is not above chance, so neither the reproduced nor the partially reproduced rule is met. With spikes at the lost position given a neighbouring position, as in the first version, Rat1 had 13 of 25 (0.52), which gave partially_reproduced. Rat1 FD9 is close to the bound. 6 units have p between 0.01 and 0.1, repeats with 2000 shuffles and five other seeds give 11 or 12 of 25 (0.44 to 0.48), and the run of 200 shuffles in the data check, with the same lookup, gives 13 of 25 (0.52); across these seven runs the count is 11 to 13 of 25, on both sides of 0.5, so the outcome for Rat1 is not robust. The outcome follows the pre-specified run of 500 shuffles, with which the five repeats of 2000 shuffles agree. Rat2 FD9 gives 2 or 3 of 28 in every repeat. Shifted spikes are dropped for lack of a position more often in Rat2's ES epochs (median 0.307 on FD9) than in Rat1's (0.074), but a count-matched variant gives the same counts for Rat2. Rat2's units are not selective with the shared position trace in any window, and Rat1's units are selective in Rat2's FD4 ES epoch (6 of 15), so the trace in Rat2's epochs may not be Rat2's position; the files do not name the animal tracked. On flight day 4, 10 of 20 Rat1 units, 0 of 16 Rat2 units, and 10 of 16 and 1 of 19 Rat3 units in its two ES epochs are significant. In MC epochs 0 to 2 units per session are significant. The "three orthogonal surfaces" part of the abstract is tested apart, and blocked.
How the test differed from the paper’s method
- The paper's Methods were not available; the selection (50 spikes at a known position), the 32 x 32 binning, the shuffle and the thresholds are common choices fixed in the claims file.
- Occupancy is the original analysis's occupancy map for the epoch, and shuffled spikes take the nearest position sample within 0.25 s, as the dandiset gives position only at spike times. A spike whose nearest sample is the lost position is dropped.
- Robust is read as at least half of the units significant in each flight day 9 session.
- Rat2's flight day 9 session is judged although whose position the trace holds in it could not be established.
ReproducedMain text, paragraph beginning "The mean spatial-information content for all 7", sentence 2; Figure 3a,b and legend
For rat 3 on flight day 4, most of the 7 cells kept the same firing fields in a third session that followed the second immediately; the fourth cell lost its field, and a few other cells gained a field in session 3.
Another recording session followed immediately, and most cells maintained the same firing fields in both sessions (Fig. 3b), demonstrating that the spatial tuning was stable across different exposures to the track.
Main text, paragraph beginning "The mean spatial-information content for all 7", sentence 2; Figure 3a,b and legend
In Rat3's two flight day 4 ES epochs, the 15 units with 50 or more spikes in each have a median rate-map correlation of 0.537 (range -0.107 to 0.849), above the 95th percentile of 1000 re-paired medians (0.102, p = 0.001) and above 0.5; 8 of 15 exceed 0.5. With smoothing of 0.5 to 2 bins and 50 or 100 spikes the median is 0.315 to 0.707, always above its null (p = 0.001); at 0.5 bins it is below 0.5. Mean rates are related across the epochs (Spearman rho 0.598, re-paired 95th percentile 0.339), consistent with the same neurons but not showing it. The dandiset's rate maps paired by their ~N names give a median of 0.157, as the names do not identify cells. In the second epoch 1 of 19 units is significant against 10 of 16 in the first, with similar occupancy and shuffle drops and more spikes per tested unit in the second (median 455 against 301); this is not explained. The original spike files in OSD-968 hold waveform amplitudes for each spike, according to the conversion notes, and could test the identity assumption; they were not used.
How the test differed from the paper’s method
- Only the title of Figure 3 was available; which sessions it compares is unknown. The test uses the only pair of same-track sessions with position on one day.
- Assumes that a tetrode and cluster id names the same neuron in both epochs; the dandiset does not say so and holds no waveforms to check it.

Not tested in a notebook 1

1 metadata insufficient

BlockedMain text, paragraph beginning "It is interesting to note", sentence 2; also the standfirst· Metadata insufficient
Hippocampal cells formed distinct, reliable representations of position on the three orthogonal surfaces of the Escher staircase in microgravity.
Thus hippocampal cells can form unique, reliable representations of position on three orthogonal surfaces in microgravity
Main text, paragraph beginning "It is interesting to note", sentence 2; also the standfirst
The dandiset holds one two-dimensional pixel position per time from one camera. Nothing in the files or the dandiset metadata describes the camera's view or the track layout, and the conversion code describes the ES track only as a three-dimensional track with 90 degree yaw and pitch turns and the position as video tracker pixel coordinates (its lines are printed in the notebook), so pixels cannot be assigned to the three surfaces. The NASA record of the study (OSD-968) says position was recorded with two synchronised cameras (printed in the notebook); a second view is not in the dandiset.

Findings about the data

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

Metadata errorThe Rat1 and Rat2 files of each flight day hold the same position trace (98.6 to 98.8% of samples at common timestamps within 2 pixels), presented as each rat's position. Rat1's units are spatially selective with it, Rat2's are not in any window, and Rat1's units are also selective in Rat2's flight day 4 ES epoch. Each file samples the trace at its own units' spike times, and the files do not name the animal the tracker followed. Whose position the trace is during Rat2's task epochs is not stated and could not be established.
Data missingPosition is given only at spike times (taken from the spike files), so occupancy cannot be computed from the files' position, and the preflight files have no position at all.
Metadata errorThe dandiset description says the preflight recordings were made on a flat rectangular track, but the preflight files label their epochs ES (Escher staircase) and MC (Magic Carpet) and hold ES and MC rate maps, as the flight files do. Which apparatus the preflight epochs were recorded on is not stated in the files.
Identifier missingThe rate-map `source_file` names are Windows 8.3 short names (ESCELL~1 to ~4, then hashed names such as ES2BC0~1), so `cell_number`, read from the ~N suffix, is not a cell number. It equals the cluster id of the best-matching unit in 84 of 211 unit-epochs, and the rate maps cannot be linked to units as the table's description says. The long names are in the NASA archive (OSD-968), whose description names files like BL2.cell5.
Description missingThe rate maps are smoothed (in the median well-matched map, 91% of the bins with a positive rate hold no spike of the unit), and the kernel is not stated.
Description missingRate maps use -999 for unvisited bins, which the column description (rate in Hz) does not state. The tracker's lost position (0, 255), 5 to 12% of position samples, is counted in the original occupancy maps (bin [63, 0], up to 19% of an occupancy map in flight).
OtherEight rate maps are identical copies of another map in the same file, some stored under a different tetrode (for example Rat1 FD4 TT1 and TT11 ESCELL~1, and four maps of Rat2 FD4 under TT13, TT19 and TT22).
Description missingUnits merge per-epoch spike files that share a tetrode and cluster id; nothing states that a cluster id names the same neuron in different epochs. The unit table lacks the `session_type` and `source_file` columns the conversion's README lists, so a unit's spikes cannot be traced to their spike file.
Data missingThe dandiset's description reports normal theta and sharp waves and ripples in the hippocampal EEG, but no EEG is in the dandiset.
OtherSpike times are given to 10 ms in five files and to 1 ms or finer in three; 2 to 15% of within-unit intervals are zero, in every epoch type and not mainly in overlapping epochs; their cause is not resolved. In the Rat1 flight day 4 file two baseline epochs overlap (2525 to 3390 s and 2720 to 3390 s).
Description missingThe age is "/" for every subject, and the position's pixel scale and camera view are not described.

Notebooks

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

Reproduction Place cells during space flight on the Neurolab mission (Knierim et al. 2000)

Tests the findings of Knierim, McNaughton and Poe (2000) that can be tested on dandiset 001754, which holds sorted units, task epochs, rate maps and spike-time positions of three rats recorded before and during the Neurolab shuttle mission. It tests spatial selectivity on the Escher staircase in flight, spatial information in flight against preflight, and the stability of place fields across two sessions. The paper is not open access; claims come from its abstract, its figure titles and the dandiset's description. There is no EEG in the dandiset. All files

Reproducing Knierim et al. (2000) from dandiset 001754
reproduce_knierim_2000.ipynbExecuted, with outputs · Source

Verification

Round 1
2026-10-14Agreed with 3 of 3 outcomes. Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook). Reviewed: The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper's abstract and figure titles from the publisher's page (the paper is not open access). The verifier checked the archive's asset metadata for the blocked claims and ran synthetic checks of skaggs_info, rma_info, merge_bins, bin_xy and PositionLookup.
Round 2
2026-10-14
Agreed with 2 of 3 outcomes. Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook). Reviewed: The full executed notebook of the first revision, with its conclusions and summary, the helper module, the claims file, the README and this attempt record, with the paper's abstract and figure titles from the publisher's page.
- flight-spatial-code: the verifier’s outcome was “Not reproduced”. Agrees with the proposed not_reproduced and no longer with partially_reproduced. The pre-specified run gives Rat1 FD9 12 of 25 (0.48) and Rat2 FD9 3 of 28 (p 0.16), and the criterion maps that to not_reproduced; the five repeats with 2000 shuffles give 11 or 12 of 25. The result still sits on the 0.5 bound, as cell 23, with the corrected lookup and 200 shuffles, gives 13 of 25 (0.52), and the conclusions, the summary and the proposed reason leave it out; across the seven runs the count is 11 to 13 of 25, which straddles the bound, so the proposed not_reproduced is not robust. Whose position the trace holds in Rat2's epochs is disclosed but unresolved, and decides whether Rat2 FD9 is a valid judged session.
Round 3
2026-10-14Agreed with 1 of 1 outcomes. Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook). Reviewed: The proposed change of flight-spatial-code to not_reproduced, with the full executed notebook of the second revision, the helper module, the claims file and this attempt record.

Method differences

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

The paper's Methods were not available; the selection (50 spikes at a known position), the 32 x 32 binning, the shuffle and the thresholds are common choices fixed in the claims file.flight-spatial-code
Occupancy is the original analysis's occupancy map for the epoch, and shuffled spikes take the nearest position sample within 0.25 s, as the dandiset gives position only at spike times. A spike whose nearest sample is the lost position is dropped.flight-spatial-code
Robust is read as at least half of the units significant in each flight day 9 session.flight-spatial-code
Rat2's flight day 9 session is judged although whose position the trace holds in it could not be established.flight-spatial-code
Only the title of Figure 3 was available; which sessions it compares is unknown. The test uses the only pair of same-track sessions with position on one day.fig3-stability-across-sessions
Assumes that a tetrode and cluster id names the same neuron in both epochs; the dandiset does not say so and holds no waveforms to check it.fig3-stability-across-sessions

Provenance

Attempt record: 001754-knierim-2000-01
Paper: Three-dimensional spatial selectivity of hippocampal neurons during space flight
Date: 2026-10-14
Made by: An agent, run by CatalystNeuro
Dataset: DANDI:001754
Version: 0.260728.1352 (doi:10.48324/dandi.001754/0.260728.1352)
Run on: GitHub Actions
Harness: Claude Code (GitHub Actions)
Model: claude-opus-5-5
Protocol: pilot-6

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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