Recordings / M13Rec001 / Run
M13Rec001, run d524f527
Status done, stage done; requested by project lead; worker [not recorded]; started 2026-10-27 02:31 UTC, finished 2026-10-27 02:33 UTC, 118 s; signature 58d28484
Stages
| Stage | Started | Seconds |
|---|---|---|
| [no stage log; run predates stage timing] | ||
Log
| Time | Agent | Action | Detail |
|---|---|---|---|
| 02:31:52 | runs | run started | {"recording_id": "55cb4aa3-6502-45a6-a14c-85cb676fe8c3", "run_id": "d524f527-48e8-4b73-be5c-3015b38033de"} |
| 02:33:50 | runs | signature written | {"criteria": "provisional", "holds": {"persistent_rotors": false, "singularities": true}, "run_id": "d524f527-48e8-4b73-be5c-3015b38033de", "signature_id": "58d28484-0e00-4312-8905-31711a0b4fb6"} |
Entries from the audit log for this run; new rows and stage changes arrive by realtime while the run is open (connecting).
Pipeline check
[no pipeline check stored for this run]
Inspector
This is an ex vivo optogenetic mouse whole-heart optical mapping recording associated with spiral-wave termination experiments. Use 1000 Hz: the linked paper states 64 × 64 camera acquisition at 1 kHz, and the deposit’s 64 × 55 frame size is consistent with a cropped version; this agrees with the frame rate already on record. The deposited movie is not truly raw camera output: depositor documentation and measurements indicate masking, temporal/spatial smoothing, and normalization. Polarity is robustly inverted, so depolarization appears as a downward deflection. Illumination was already on before frame 0 and turned off at frame 4977; the frame-3170 image step should be treated as a fluorescence baseline/rhythm-change event with provisional interpretation as spiral termination, not as light onset.
| Measurement | Value | Method, Caveat |
|---|---|---|
| SNR, median (p10–p90) | 32.5 (26.9–44.9) | assumes white noise; on temporally smoothed deposits noise is underestimated and SNR inflated |
| Mask coverage | 66.2%, 2332 of 3520 px | depositor NaN mask (frame 0) |
| Polarity | blocks 18, inverted True, blocks agreeing 18, median dvdt skew -4.419912338256836 | sign of median per-pixel skew of dV/dt, baseline-corrected (121 frames) |
| Drift / bleaching | baseline change -1.61, vs beat amplitude -1.12, slow range 3.33, trend, Spearman -0.489 | running median (927 frames) of the tissue-mean raw signal; steps from events (light, rhythm change) and depositor normalization or drift removal change or erase the baseline; bleaching cannot be separated from them here |
| Prior processing | negative values, nan mask all frames, temporal smoothing, spatial smoothing | deposit checks |
| Dominant cycle by block, frames | 0–1000: 66.7, 1000–2000: 66.7, 2000–3000: 52.6, 3000–4000: 83.3, 4000–5000: 100.0, 5000–6000: 142.9, 6000–7000: 100.0, 7000–8000: 142.9, 8000–9000: 83.3 |
| Concern | Severity | Detail |
|---|---|---|
| Pre-deposit processing / raw-data label | warn | The README labels M13Rec001 as raw experimental data, but the notebook documents masking, spatial smoothing, temporal smoothing, and normalization with Python Analyser; prior_processing measurements support processed data. Analyses requiring raw photon counts or independent pixel noise would be misleading if this is treated as raw camera data. |
| Event interpretation at frame 3170 | warn | The image event at frame 3170 is a baseline_step only. The DAQ shows illumination began before frame 0 and ended at frame 4977, so treating frame 3170 as light onset would be wrong. The stored spiral-termination label is a provisional interpretation from timing relative to the paper, not a direct measurement. |
| Baseline and illumination artifact | warn | The publication reports blue stimulation light crosstalk causing an increase in fluorescence baseline and re-normalization by division to the recorded stimulation light signal; the recording also has a large slow baseline range and a baseline step. Analyses using absolute baseline or amplitude should account for illumination/crosstalk/normalization effects. |
| Provisional tool thresholds | info | Event detection, processing flags, SNR, rhythm, and reference-rate thresholds are provisional and not yet reviewed by a domain scientist; conclusions depending on them should be checked for critical analyses. |
| Event | Frame | Source | Method |
|---|---|---|---|
| illumination on | 0 ± 11 | acquisition log | midpoint threshold on DAQ channel 'led_trigger', mapped to frames via camera triggers |
| illumination off | 4977 ± 11 | acquisition log | midpoint threshold on DAQ channel 'led_trigger', mapped to frames via camera triggers |
| baseline step | 3170 ± 17 | image | consensus upward step in running-median baseline of tissue-mean raw signal |
Inspector report 2026-10-27 20:27 UTC, model openai:gpt-5.5, provisional. Per-pixel SNR is high by the provisional metric: median = 32.506531024253725, p10 = 26.87502130582481, p90 = 44.884363625066875 over 3000 frames. Because the deposit is documented and measured as temporally smoothed, the tool caveat applies: white-noise assumptions can underestimate noise and inflate SNR. The depositor NaN mask in frame 0 contains 2332 tissue pixels out of 3520 total pixels, coverage = 0.6625, with 1188 NaN pixels. Acquisition log detects illumination already on at the first deposited frame: led_trigger transition occurred before_first_frame, 23.0 frames before frame 0, reported as illumination_on at frame 0 with uncertainty 11 frames; photodiode agrees. Acquisition log detects illumination_off at frame 4977 with uncertainty 11 frames; photodiode agrees. Image analysis detects a baseline_step at frame 3170 with uncertainty 17 frames: this measurement only shows the tissue-mean fluorescence baseline changed, not illumination onset. A stored project-lead interpretation, citing Hussaini et al. 2023 Fig 2C, labels the frame-3170 step as “spiral termination under illumination”; the source caveat says the paper does not name M13Rec001 and the termination assignment is inferred from timing, so it should be treated as provisional interpretation, not a direct measurement. The stored image-based “illumination_on” at frame 3170 is contradicted by the DAQ led_trigger and photodiode, which show light already on from before frame 0 until frame 4977. The tissue-mean slow baseline changes substantially: baseline_start = 1.439404845237732, baseline_end = -0.17559432983398438, baseline_change = -1.6149991750717163, which is -1.1213198412261043 times the beat amplitude; slow_baseline_range = 3.3284222781658173 and monotonic_trend_spearman = -0.4894475048599732. The tool cautions that steps from events, rhythm change, depositor normalization, or drift removal affect the baseline, so bleaching cannot be separated here.
Range checks
| Metric | Segment | Value at Run Setting | Cited Range | Status |
|---|---|---|---|---|
| [no critic verdict for this run] | ||||
Compare with run b646e930
A: this run, code da0b6c7, None workers. B: run b646e930, 2026-10-27 02:14 UTC, code 9f18ba0, None workers. 63 stored values differ.
| File | A | B | Same | How |
|---|---|---|---|---|
| frames/voltage | [none] | [none] | [not comparable] | recorded sha256 |
| frames/phase | [none] | [none] | [not comparable] | recorded sha256 |
| frames/maps | [none] | [none] | [not comparable] | recorded sha256 |
| movie.mp4 | 2926877 | 2866041 | no | size in bytes only; frames not compared |
| Stored Value | A | B |
|---|---|---|
| metrics.computed_on.rotors | [absent] | phase of spatially filtered signal |
| metrics.computed_on.singularities_and_rotors | phase of spatially filtered signal | [absent] |
| metrics.min_rotor_frames | 52 | [absent] |
| metrics.paired_singularity_frac | 0.037037037037037035 | [absent] |
| metrics.persistent_rotor_count_max | 1 | [absent] |
| metrics.persistent_rotor_frames_frac | 0.043333333333333335 | [absent] |
| metrics.persistent_rotor_lifetimes | [78] | [absent] |
| metrics.persistent_rotor_tracks | 1 | [absent] |
| metrics.rotor_count_max | [absent] | 4 |
| metrics.rotor_count_mean | [absent] | 0.27 |
| metrics.rotor_frames_frac | [absent] | 0.18333333333333332 |
| metrics.segments | {'after_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.09469026548672567, 'singularity_frames_frac': 0.05663716814159292, 'persistent_rotor_count_max': 0, 'persistent_rotor_frames_frac': 0.0}, 'before_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.5656716417910448, 'singularity_frames_frac': 0.3970149253731343, 'persistent_rotor_count_max': 1, 'persistent_rotor_frames_frac': 0.11641791044776119}} | [absent] |
| metrics.singularity_count_max | 4 | [absent] |
| metrics.singularity_count_mean | 0.27 | [absent] |
| metrics.singularity_frames_frac | 0.18333333333333332 | [absent] |
| metrics.tracks | 119 | [absent] |
| filter_params.tracking | {'link_px': 4.0, 'max_gap': 5, 'min_cycles': 1.0, 'min_frames': 52, 'paired_frac': 0.5, 'pair_dist_px': 3.0} | [absent] |
| filter_params.window.illumination_on | {'frame': 3170, 'detected': True, 'event_id': '42ba71e2-c2c4-4833-abc2-467506ec90a1', 'uncertainty_frames': 17} | [absent] |
| filter_params.window.light_on_frame | [absent] | 3200 |
| filter_params.window.segment_cycles_frames | {'after_light': 141, 'before_light': 52} | [absent] |
| filter_params.window.segments.after_light[0] | 3170 | 3200 |
| filter_params.window.segments.before_light[1] | 3170 | 3200 |
| sensitivity.criterion | [absent] | at every level: frac(before_light) >= 0.1 and >= 2.0 x frac(after_light) |
| sensitivity.finding | [absent] | rotor-frame fraction higher in 'before_light' than 'after_light' |
| sensitivity.findings | {'singularities': {'finding': "singularities more frequent in 'before_light' than 'after_light'", 'criterion': 'frac(before_light) >= 0.1 and >= 2.0 x frac(after_light), at every level', 'holds_across_filters': True, 'label_across_filters': 'holds (provisional)'}, 'persistent_rotors': {'finding': "persistent rotors more frequent in 'before_light' than 'after_light'", 'criterion': 'frac(before_light) >= 0.1 and >= 2.0 x frac(after_light), at every level', 'holds_across_filters': False, 'label_across_filters': 'does not hold (provisional)', 'holds_across_trackers': False, 'label_across_trackers': 'does not hold (provisional)'}} | [absent] |
| sensitivity.fixed.baseline_frames | [absent] | 121 |
| sensitivity.fixed.baseline_method | [absent] | scipy.ndimage.uniform_filter1d, mode=reflect, subtracted per pixel |
| sensitivity.fixed.lowpass | [absent] | None |
| sensitivity.fixed.mask | [absent] | not NaN in frame 0 and nonzero temporal std |
| sensitivity.fixed.min_rotor_frames | 52 | [absent] |
| sensitivity.fixed.pad_frames | [absent] | 200 |
| sensitivity.fixed.phase_method | [absent] | angle of scipy.signal.hilbert along time, on spatially filtered signal |
| sensitivity.fixed.polarity_method | [absent] | sign of median per-pixel skew of dV/dt on baseline-corrected signal |
| sensitivity.fixed.segments | {'after_light': [3170, 4300], 'before_light': [2500, 3170]} | [absent] |
| sensitivity.fixed.spatial_applies_to | [absent] | phase/activation only; displayed voltage is baseline-corrected only |
| sensitivity.fixed.spatial_method | [absent] | scipy.ndimage.gaussian_filter per frame, mode=reflect; NaN set to 0 before filtering, non-tissue zeroed after |
| sensitivity.fixed.spatial_truncate | [absent] | 4.0 |
| sensitivity.fixed.window | [2500, 4300] | [absent] |
| sensitivity.grid | [{'sigma': 'light', 'baseline': 'light', 'findings': {'singularities': {'after': 0.0584070796460177, 'holds': True, 'label': 'holds (provisional)', 'ratio': 6.439620081411126, 'before': 0.3761194029850746}, 'persistent_rotors': {'after': 0.0, 'holds': False, 'label': 'does not hold (provisional)', 'ratio': None, 'before': 0.08059701492537313}}, 'segments': {'after_light': {'singularity_count_max': 12, 'singularity_count_mean': 0.13008849557522123, 'singularity_frames_frac': 0.0584070796460177, 'persistent_rotor_count_max': 0, 'persistent_rotor_frames_frac': 0.0}, 'before_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.5402985074626866, 'singularity_frames_frac': 0.3761194029850746, 'persistent_rotor_count_max': 1, 'persistent_rotor_frames_frac': 0.08059701492537313}}, 'spatial_sigma': 0.5, 'baseline_frames': 241, 'persistent_rotor_tracks': 1}, {'sigma': 'default', 'baseline': 'light', 'findings': {'singularities': {'after': 0.05663716814159292, 'holds': True, 'label': 'holds (provisional)', 'ratio': 6.53544776119403, 'before': 0.3701492537313433}, 'persistent_rotors': {'after': 0.0, 'holds': False, 'label': 'does not hold (provisional)', 'ratio': None, 'before': 0.08059701492537313}}, 'segments': {'after_light': {'singularity_count_max': 8, 'singularity_count_mean': 0.11150442477876106, 'singularity_frames_frac': 0.05663716814159292, 'persistent_rotor_count_max': 0, 'persistent_rotor_frames_frac': 0.0}, 'before_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.5313432835820896, 'singularity_frames_frac': 0.3701492537313433, 'persistent_rotor_count_max': 1, 'persistent_rotor_frames_frac': 0.08059701492537313}}, 'spatial_sigma': 1.0, 'baseline_frames': 241, 'persistent_rotor_tracks': 1}, {'sigma': 'heavier', 'baseline': 'light', 'findings': {'singularities': {'after': 0.05398230088495575, 'holds': True, 'label': 'holds (provisional)', 'ratio': 6.58037680450208, 'before': 0.35522388059701493}, 'persistent_rotors': {'after': 0.0, 'holds': False, 'label': 'does not hold (provisional)', 'ratio': None, 'before': 0.08059701492537313}}, 'segments': {'after_light': {'singularity_count_max': 6, 'singularity_count_mean': 0.09469026548672567, 'singularity_frames_frac': 0.05398230088495575, 'persistent_rotor_count_max': 0, 'persistent_rotor_frames_frac': 0.0}, 'before_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.48955223880597015, 'singularity_frames_frac': 0.35522388059701493, 'persistent_rotor_count_max': 1, 'persistent_rotor_frames_frac': 0.08059701492537313}}, 'spatial_sigma': 2.0, 'baseline_frames': 241, 'persistent_rotor_tracks': 1}, {'sigma': 'light', 'baseline': 'default', 'findings': {'singularities': {'after': 0.05929203539823009, 'holds': True, 'label': 'holds (provisional)', 'ratio': 6.746268656716419, 'before': 0.4}, 'persistent_rotors': {'after': 0.0, 'holds': True, 'label': 'holds (provisional)', 'ratio': None, 'before': 0.11641791044776119}}, 'segments': {'after_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.10442477876106195, 'singularity_frames_frac': 0.05929203539823009, 'persistent_rotor_count_max': 0, 'persistent_rotor_frames_frac': 0.0}, 'before_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.5716417910447761, 'singularity_frames_frac': 0.4, 'persistent_rotor_count_max': 1, 'persistent_rotor_frames_frac': 0.11641791044776119}}, 'spatial_sigma': 0.5, 'baseline_frames': 121, 'persistent_rotor_tracks': 1}, {'sigma': 'default', 'baseline': 'default', 'findings': {'singularities': {'after': 0.05663716814159292, 'holds': True, 'label': 'holds (provisional)', 'ratio': 7.009794776119403, 'before': 0.3970149253731343}, 'persistent_rotors': {'after': 0.0, 'holds': True, 'label': 'holds (provisional)', 'ratio': None, 'before': 0.11641791044776119}}, 'segments': {'after_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.09469026548672567, 'singularity_frames_frac': 0.05663716814159292, 'persistent_rotor_count_max': 0, 'persistent_rotor_frames_frac': 0.0}, 'before_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.5656716417910448, 'singularity_frames_frac': 0.3970149253731343, 'persistent_rotor_count_max': 1, 'persistent_rotor_frames_frac': 0.11641791044776119}}, 'spatial_sigma': 1.0, 'baseline_frames': 121, 'persistent_rotor_tracks': 1}, {'sigma': 'heavier', 'baseline': 'default', 'findings': {'singularities': {'after': 0.049557522123893805, 'holds': True, 'label': 'holds (provisional)', 'ratio': 7.529317697228145, 'before': 0.373134328358209}, 'persistent_rotors': {'after': 0.0, 'holds': True, 'label': 'holds (provisional)', 'ratio': None, 'before': 0.11492537313432835}}, 'segments': {'after_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.07168141592920355, 'singularity_frames_frac': 0.049557522123893805, 'persistent_rotor_count_max': 0, 'persistent_rotor_frames_frac': 0.0}, 'before_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.5238805970149254, 'singularity_frames_frac': 0.373134328358209, 'persistent_rotor_count_max': 1, 'persistent_rotor_frames_frac': 0.11492537313432835}}, 'spatial_sigma': 2.0, 'baseline_frames': 121, 'persistent_rotor_tracks': 1}, {'sigma': 'light', 'baseline': 'heavier', 'findings': {'singularities': {'after': 0.05398230088495575, 'holds': True, 'label': 'holds (provisional)', 'ratio': 7.382187423538047, 'before': 0.39850746268656717}, 'persistent_rotors': {'after': 0.0, 'holds': True, 'label': 'holds (provisional)', 'ratio': None, 'before': 0.20597014925373133}}, 'segments': {'after_light': {'singularity_count_max': 7, 'singularity_count_mean': 0.09911504424778761, 'singularity_frames_frac': 0.05398230088495575, 'persistent_rotor_count_max': 0, 'persistent_rotor_frames_frac': 0.0}, 'before_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.5283582089552239, 'singularity_frames_frac': 0.39850746268656717, 'persistent_rotor_count_max': 1, 'persistent_rotor_frames_frac': 0.20597014925373133}}, 'spatial_sigma': 0.5, 'baseline_frames': 81, 'persistent_rotor_tracks': 1}, {'sigma': 'default', 'baseline': 'heavier', 'findings': {'singularities': {'after': 0.05398230088495575, 'holds': True, 'label': 'holds (provisional)', 'ratio': 7.354538781502324, 'before': 0.3970149253731343}, 'persistent_rotors': {'after': 0.0, 'holds': True, 'label': 'holds (provisional)', 'ratio': None, 'before': 0.20597014925373133}}, 'segments': {'after_light': {'singularity_count_max': 6, 'singularity_count_mean': 0.09115044247787611, 'singularity_frames_frac': 0.05398230088495575, 'persistent_rotor_count_max': 0, 'persistent_rotor_frames_frac': 0.0}, 'before_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.5268656716417911, 'singularity_frames_frac': 0.3970149253731343, 'persistent_rotor_count_max': 1, 'persistent_rotor_frames_frac': 0.20597014925373133}}, 'spatial_sigma': 1.0, 'baseline_frames': 81, 'persistent_rotor_tracks': 1}, {'sigma': 'heavier', 'baseline': 'heavier', 'findings': {'singularities': {'after': 0.04601769911504425, 'holds': True, 'label': 'holds (provisional)', 'ratio': 8.36796785304248, 'before': 0.3850746268656716}, 'persistent_rotors': {'after': 0.0, 'holds': True, 'label': 'holds (provisional)', 'ratio': None, 'before': 0.21044776119402986}}, 'segments': {'after_light': {'singularity_count_max': 6, 'singularity_count_mean': 0.06991150442477877, 'singularity_frames_frac': 0.04601769911504425, 'persistent_rotor_count_max': 0, 'persistent_rotor_frames_frac': 0.0}, 'before_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.4955223880597015, 'singularity_frames_frac': 0.3850746268656716, 'persistent_rotor_count_max': 1, 'persistent_rotor_frames_frac': 0.21044776119402986}}, 'spatial_sigma': 2.0, 'baseline_frames': 81, 'persistent_rotor_tracks': 1}] | [absent] |
| sensitivity.holds | {'singularities': True, 'persistent_rotors': False} | True |
| sensitivity.levels | [absent] | {'light': {'holds': True, 'ratio': 6.285714285714286, 'segments': {'after_light': {'rotor_count_max': 4, 'rotor_count_mean': 0.10727272727272727, 'rotor_frames_frac': 0.060909090909090906}, 'before_light': {'rotor_count_max': 4, 'rotor_count_mean': 0.5471428571428572, 'rotor_frames_frac': 0.38285714285714284}}, 'spatial_sigma': 0.5}, 'default': {'holds': True, 'ratio': 6.53125, 'segments': {'after_light': {'rotor_count_max': 4, 'rotor_count_mean': 0.09727272727272727, 'rotor_frames_frac': 0.05818181818181818}, 'before_light': {'rotor_count_max': 4, 'rotor_count_mean': 0.5414285714285715, 'rotor_frames_frac': 0.38}}, 'spatial_sigma': 1.0}, 'heavier': {'holds': True, 'ratio': 7.01530612244898, 'segments': {'after_light': {'rotor_count_max': 4, 'rotor_count_mean': 0.07363636363636364, 'rotor_frames_frac': 0.05090909090909091}, 'before_light': {'rotor_count_max': 4, 'rotor_count_mean': 0.5014285714285714, 'rotor_frames_frac': 0.35714285714285715}}, 'spatial_sigma': 2.0}} |
| sensitivity.status | provisional | [absent] |
| sensitivity.trackers | [{'finding': {'after': 0.0, 'holds': False, 'label': 'does not hold (provisional)', 'ratio': None, 'before': 0.0}, 'link_px': 2.0, 'max_gap': 1, 'tracker': 'strict', 'segments': {'after_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.09469026548672567, 'singularity_frames_frac': 0.05663716814159292, 'persistent_rotor_count_max': 0, 'persistent_rotor_frames_frac': 0.0}, 'before_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.5656716417910448, 'singularity_frames_frac': 0.3970149253731343, 'persistent_rotor_count_max': 0, 'persistent_rotor_frames_frac': 0.0}}, 'persistent_rotor_tracks': 0}, {'finding': {'after': 0.0, 'holds': True, 'label': 'holds (provisional)', 'ratio': None, 'before': 0.11641791044776119}, 'link_px': 4.0, 'max_gap': 5, 'tracker': 'default', 'segments': {'after_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.09469026548672567, 'singularity_frames_frac': 0.05663716814159292, 'persistent_rotor_count_max': 0, 'persistent_rotor_frames_frac': 0.0}, 'before_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.5656716417910448, 'singularity_frames_frac': 0.3970149253731343, 'persistent_rotor_count_max': 1, 'persistent_rotor_frames_frac': 0.11641791044776119}}, 'persistent_rotor_tracks': 1}, {'finding': {'after': 0.0, 'holds': True, 'label': 'holds (provisional)', 'ratio': None, 'before': 0.20298507462686566}, 'link_px': 6.0, 'max_gap': 10, 'tracker': 'loose', 'segments': {'after_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.09469026548672567, 'singularity_frames_frac': 0.05663716814159292, 'persistent_rotor_count_max': 0, 'persistent_rotor_frames_frac': 0.0}, 'before_light': {'singularity_count_max': 4, 'singularity_count_mean': 0.5656716417910448, 'singularity_frames_frac': 0.3970149253731343, 'persistent_rotor_count_max': 1, 'persistent_rotor_frames_frac': 0.20298507462686566}}, 'persistent_rotor_tracks': 1}] | [absent] |
| sensitivity.varied | {'spatial_sigma': {'light': 0.5, 'default': 1.0, 'heavier': 2.0}, 'baseline_frames': {'light': 241, 'default': 121, 'heavier': 81}, 'tracker(link_px, max_gap)': {'loose': [6.0, 10], 'strict': [2.0, 1], 'default': [4.0, 5]}} | spatial_sigma |
| sensitivity.window | [absent] | [2500, 4300] |
| criteria_status.note | [absent] | Earlier run: light-on hard-coded at frame 3200, raw singularity counts only (no persistence), spatial-sigma-only sensitivity, criterion unreviewed. Superseded; kept for provenance. |
| criteria_status.rules | length 11 | length 0 |
| criteria_status.superseded_by_run | [absent] | d524f527-48e8-4b73-be5c-3015b38033de |
| rotor_count | 1 | 4 |
| pipeline.params.polarity | -1 | [absent] |
| pipeline.params.render | {'step': 2, 'palettes': {'camera': 'gray'}, 'interpolation': 'nearest'} | [absent] |
| pipeline.params.tracking | {'link_px': 4.0, 'max_gap': 5, 'min_cycles': 1.0, 'min_frames': 52, 'paired_frac': 0.5, 'pair_dist_px': 3.0} | [absent] |
| pipeline.params.window | {'f0': 2500, 'f1': 4300, 'segments': {'after_light': [3170, 4300], 'before_light': [2500, 3170]}, 'illumination_on': {'frame': 3170, 'detected': True, 'event_id': '42ba71e2-c2c4-4833-abc2-467506ec90a1', 'uncertainty_frames': 17}, 'segment_cycles_frames': {'after_light': 141, 'before_light': 52}} | [absent] |
| pipeline.deposit_checks | {'flags': [{'flag': 'negative_values', 'value': 0.3231635934819897, 'suggests': 'baseline-subtracted or normalized; raw fluorescence counts are non-negative', 'threshold': 0.01}, {'flag': 'non_integer', 'value': 0.0, 'suggests': 'not raw camera counts (camera output is integer); weak alone', 'threshold': 0.5}, {'flag': 'nan_mask_all_frames', 'value': 1188, 'suggests': 'tissue masked by depositor; the mask is theirs'}, {'flag': 'temporal_smoothing', 'value': 0.9120054707808141, 'suggests': 'temporally low-pass filtered (white shot noise gives dV lag-1 autocorr near -0.5)', 'threshold': 0.5}, {'flag': 'spatial_smoothing', 'value': 0.9957938301611564, 'suggests': 'spatially filtered or binned (shot noise is independent between pixels)', 'threshold': 0.8}], 'status': 'provisional', 'measures': {'max': 4.49806547164917, 'min': -6.050762176513672, 'frames_used': 2000, 'integer_frac': 0.0, 'negative_frac': 0.3231635934819897, 'frames_with_nan': 9267, 'dv_lag1_autocorr_median': 0.9120054707808141, 'neighbour_dv_corr_median': 0.9957938301611564}, 'processed_before_deposit': True} | None |
| pipeline.steps | length 11 | length 8 |
| pipeline.steps[1] | deposit_checks | baseline_correct |
| pipeline.steps[2] | detect_events | polarity |
| pipeline.steps[3] | baseline_correct | spatial_filter(phase only) |
| pipeline.steps[4] | polarity | hilbert_phase |
| pipeline.steps[5] | spatial_filter(phase only) | phase_singularities |
| pipeline.steps[6] | hilbert_phase | sensitivity |
| pipeline.steps[7] | phase_singularities | render |
| methods_text | Recording Mouse heart, spiral wave and optogenetic termination (M13Rec001) (doi:10.5281/zenodo.10228296; 64x55 px, 9267 frames, frame rate not stated) was analysed over frames 2500-4300. Deposit shows signs of prior processing (provisional): negative values, non integer, nan mask all frames, temporal smoothing, spatial smoothing. Each pixel was baseline-corrected by subtracting a 121-frame centered moving average; NaN pixels were set to zero. Dye polarity (inverted) was taken from the sign of the median per-pixel skew of dV/dt. For phase only, each frame was spatially filtered with a Gaussian (sigma 1.0 px, truncated at 4.0 sigma); no temporal low-pass was applied. Phase was the angle of the Hilbert transform, computed with 200 frames of padding on each side. Phase singularities were plaquettes with |winding| > 0.9 turns at least 3 px inside the tissue edge; they were tracked across frames (same charge, <= 4.0 px per frame, gaps <= 5 frames), and a persistent rotor was a track lasting >= 52 frames (one cycle of the fastest segment) that was within 3.0 px of an opposite-charge singularity in no more than 50% of its frames. Illumination onset was detected at frame 3170 (+/- 17) as a step in the tissue-mean raw baseline (provisional detector); segments: before_light 2500-3170, after_light 3170-4300. Sensitivity: baseline 241, 121, 81 frames x sigma 0.5, 1.0, 2.0 px, and tracker variants. Finding 'singularities more frequent in 'before_light' than 'after_light'': across filters holds (provisional). Finding 'persistent rotors more frequent in 'before_light' than 'after_light'': across filters does not hold (provisional); across trackers does not hold (provisional). All thresholds and criteria are provisional pending review by a domain scientist. | Recording Mouse heart, spiral wave and optogenetic termination (M13Rec001) (doi:10.5281/zenodo.10228296; 64x55 px, 9267 frames, frame rate not stated) was analysed over frames 2500-4300. Each pixel was baseline-corrected by subtracting a 121-frame centered moving average; NaN pixels were set to zero. Dye polarity (inverted) was taken from the sign of the median per-pixel skew of dV/dt. For phase only, each frame was spatially filtered with a Gaussian (sigma 1.0 px, truncated at 4.0 sigma); no temporal low-pass was applied. Phase was the angle of the Hilbert transform, computed with 200 frames of padding on each side. Phase singularities were plaquettes with |winding| > 0.9 turns at least 3 px inside the tissue edge. Sensitivity was tested by repeating detection at sigma 0.5, 1.0, 2.0 px. Criterion (at every level: frac(before_light) >= 0.1 and >= 2.0 x frac(after_light)): holds at all levels. |