Recordings / M13Rec001 / Run
M13Rec001, run bdcc4054
Status done, stage done; requested by project lead; worker [not recorded]; started 2026-10-27 20:04 UTC, finished 2026-10-27 20:06 UTC, 126 s; signature 70790eff
Stages
| Stage | Started | Seconds |
|---|---|---|
| [no stage log; run predates stage timing] | ||
Log
| Time | Agent | Action | Detail |
|---|---|---|---|
| 20:04:21 | runs | run started | {"recording_id": "55cb4aa3-6502-45a6-a14c-85cb676fe8c3", "run_id": "bdcc4054-afd1-471f-be3e-ac5130cfd37c"} |
| 20:06:26 | runs | signature written | {"criteria": "provisional", "holds": {"persistent_rotors": false, "persistent_rotors_fraction_superseded": false, "singularities": true}, "run_id": "bdcc4054-afd1-471f-be3e-ac5130cfd37c", "signature_id": "70790eff-685b-44a4-ae69-346f9e0a8fbb"} |
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 d524f527
A: this run, code 701ee65, None workers. B: run d524f527, 2026-10-27 02:31 UTC, code da0b6c7, None workers. 148 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 | 2940361 | 2926877 | no | size in bytes only; frames not compared |
| Stored Value | A | B |
|---|---|---|
| metrics.persistent_rotor_durations | [{'end': 3126, 'start': 3049, 'charge': -1, 'lifetime_cycles': 1.5, 'lifetime_frames': 78, 'frames_in_segment': 78}] | [absent] |
| metrics.persistent_rotors | 1 | [absent] |
| metrics.segments.after_light | [absent] | {'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} |
| metrics.segments.after_step | {'persistent_rotors': 0, 'singularity_count_max': 4, 'singularity_count_mean': 0.09469026548672567, 'singularity_frames_frac': 0.05663716814159292, 'persistent_rotor_count_max': 0, 'persistent_rotor_durations': [], 'persistent_rotor_frames_frac': 0.0} | [absent] |
| metrics.segments.before_light | [absent] | {'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} |
| metrics.segments.before_step | {'persistent_rotors': 1, 'singularity_count_max': 4, 'singularity_count_mean': 0.5656716417910448, 'singularity_frames_frac': 0.3970149253731343, 'persistent_rotor_count_max': 1, 'persistent_rotor_durations': [{'end': 3126, 'start': 3049, 'charge': -1, 'lifetime_cycles': 1.5, 'lifetime_frames': 78, 'frames_in_segment': 78}], 'persistent_rotor_frames_frac': 0.11641791044776119} | [absent] |
| filter_params.window.illumination | Acquisition log (0111210010.txt, LED trigger channel, provisional interpretation): illumination on throughout the analysed frames 2500-4300. | [absent] |
| filter_params.window.illumination_on | [absent] | {'frame': 3170, 'detected': True, 'event_id': '42ba71e2-c2c4-4833-abc2-467506ec90a1', 'uncertainty_frames': 17} |
| filter_params.window.segment_cycles_frames.after_light | [absent] | 141 |
| filter_params.window.segment_cycles_frames.after_step | 141 | [absent] |
| filter_params.window.segment_cycles_frames.before_light | [absent] | 52 |
| filter_params.window.segment_cycles_frames.before_step | 52 | [absent] |
| filter_params.window.segments.after_light | [absent] | [3170, 4300] |
| filter_params.window.segments.after_step | [3170, 4300] | [absent] |
| filter_params.window.segments.before_light | [absent] | [2500, 3170] |
| filter_params.window.segments.before_step | [2500, 3170] | [absent] |
| filter_params.window.split_event | {'kind': 'baseline_step', 'cause': 'not established', 'frame': 3170, 'source': 'image', 'event_id': '46c59a51-1a01-4aed-8021-db9a63720a1d', 'uncertainty_frames': 17} | [absent] |
| sensitivity.findings.persistent_rotors.criterion | count(before) >= 1 and count(after) <= 0, with before='before_step', after='after_step', at every setting | frac(before_light) >= 0.1 and >= 2.0 x frac(after_light), at every level |
| sensitivity.findings.persistent_rotors.finding | persistent rotors in 'before_step' but not (or less in) 'after_step' | persistent rotors more frequent in 'before_light' than 'after_light' |
| sensitivity.findings.persistent_rotors.holds_across_filters | True | False |
| sensitivity.findings.persistent_rotors.label_across_filters | holds (provisional) | does not hold (provisional) |
| sensitivity.findings.persistent_rotors_fraction_superseded | {'finding': "persistent rotors in 'before_step' but not (or less in) 'after_step'", 'criterion': "frac(before) >= 0.1 and >= 2.0 x frac(after) (superseded: fraction rule applied to persistent rotors), with before='before_step', after='after_step', at every setting", 'superseded': True, 'holds_across_filters': False, 'label_across_filters': 'does not hold (provisional)', 'holds_across_trackers': False, 'label_across_trackers': 'does not hold (provisional)'} | [absent] |
| sensitivity.findings.singularities.criterion | frac(before) >= 0.1 and >= 2.0 x frac(after), with before='before_step', after='after_step', at every setting | frac(before_light) >= 0.1 and >= 2.0 x frac(after_light), at every level |
| sensitivity.findings.singularities.finding | singularities in 'before_step' but not (or less in) 'after_step' | singularities more frequent in 'before_light' than 'after_light' |
| sensitivity.fixed.segments.after_light | [absent] | [3170, 4300] |
| sensitivity.fixed.segments.after_step | [3170, 4300] | [absent] |
| sensitivity.fixed.segments.before_light | [absent] | [2500, 3170] |
| sensitivity.fixed.segments.before_step | [2500, 3170] | [absent] |
| sensitivity.grid[0].findings.persistent_rotors.before | 1 | 0.08059701492537313 |
| sensitivity.grid[0].findings.persistent_rotors.holds | True | False |
| sensitivity.grid[0].findings.persistent_rotors.label | holds (provisional) | does not hold (provisional) |
| sensitivity.grid[0].findings.persistent_rotors.lifetimes_frames | {'after_step': [], 'before_step': [54]} | [absent] |
| sensitivity.grid[0].findings.persistent_rotors.ratio | [absent] | None |
| sensitivity.grid[0].findings.persistent_rotors_fraction_superseded | {'after': 0.0, 'holds': False, 'label': 'does not hold (provisional)', 'ratio': None, 'before': 0.08059701492537313} | [absent] |
| sensitivity.grid[0].segments.after_light | [absent] | {'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} |
| sensitivity.grid[0].segments.after_step | {'persistent_rotors': 0, 'singularity_count_max': 12, 'singularity_count_mean': 0.13008849557522123, 'singularity_frames_frac': 0.0584070796460177, 'persistent_rotor_count_max': 0, 'persistent_rotor_durations': [], 'persistent_rotor_frames_frac': 0.0} | [absent] |
| sensitivity.grid[0].segments.before_light | [absent] | {'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} |
| sensitivity.grid[0].segments.before_step | {'persistent_rotors': 1, 'singularity_count_max': 4, 'singularity_count_mean': 0.5402985074626866, 'singularity_frames_frac': 0.3761194029850746, 'persistent_rotor_count_max': 1, 'persistent_rotor_durations': [{'end': 3046, 'start': 2993, 'charge': -1, 'lifetime_cycles': 1.04, 'lifetime_frames': 54, 'frames_in_segment': 54}], 'persistent_rotor_frames_frac': 0.08059701492537313} | [absent] |
| sensitivity.grid[1].findings.persistent_rotors.before | 1 | 0.08059701492537313 |
| sensitivity.grid[1].findings.persistent_rotors.holds | True | False |
| sensitivity.grid[1].findings.persistent_rotors.label | holds (provisional) | does not hold (provisional) |
| sensitivity.grid[1].findings.persistent_rotors.lifetimes_frames | {'after_step': [], 'before_step': [54]} | [absent] |
| sensitivity.grid[1].findings.persistent_rotors.ratio | [absent] | None |
| sensitivity.grid[1].findings.persistent_rotors_fraction_superseded | {'after': 0.0, 'holds': False, 'label': 'does not hold (provisional)', 'ratio': None, 'before': 0.08059701492537313} | [absent] |
| sensitivity.grid[1].segments.after_light | [absent] | {'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} |
| sensitivity.grid[1].segments.after_step | {'persistent_rotors': 0, 'singularity_count_max': 8, 'singularity_count_mean': 0.11150442477876106, 'singularity_frames_frac': 0.05663716814159292, 'persistent_rotor_count_max': 0, 'persistent_rotor_durations': [], 'persistent_rotor_frames_frac': 0.0} | [absent] |
| sensitivity.grid[1].segments.before_light | [absent] | {'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} |
| sensitivity.grid[1].segments.before_step | {'persistent_rotors': 1, 'singularity_count_max': 4, 'singularity_count_mean': 0.5313432835820896, 'singularity_frames_frac': 0.3701492537313433, 'persistent_rotor_count_max': 1, 'persistent_rotor_durations': [{'end': 3046, 'start': 2993, 'charge': -1, 'lifetime_cycles': 1.04, 'lifetime_frames': 54, 'frames_in_segment': 54}], 'persistent_rotor_frames_frac': 0.08059701492537313} | [absent] |
| sensitivity.grid[2].findings.persistent_rotors.before | 1 | 0.08059701492537313 |
| sensitivity.grid[2].findings.persistent_rotors.holds | True | False |
| sensitivity.grid[2].findings.persistent_rotors.label | holds (provisional) | does not hold (provisional) |
| sensitivity.grid[2].findings.persistent_rotors.lifetimes_frames | {'after_step': [], 'before_step': [54]} | [absent] |
| sensitivity.grid[2].findings.persistent_rotors.ratio | [absent] | None |
| sensitivity.grid[2].findings.persistent_rotors_fraction_superseded | {'after': 0.0, 'holds': False, 'label': 'does not hold (provisional)', 'ratio': None, 'before': 0.08059701492537313} | [absent] |
| sensitivity.grid[2].segments.after_light | [absent] | {'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} |
| sensitivity.grid[2].segments.after_step | {'persistent_rotors': 0, 'singularity_count_max': 6, 'singularity_count_mean': 0.09469026548672567, 'singularity_frames_frac': 0.05398230088495575, 'persistent_rotor_count_max': 0, 'persistent_rotor_durations': [], 'persistent_rotor_frames_frac': 0.0} | [absent] |
| sensitivity.grid[2].segments.before_light | [absent] | {'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} |
| sensitivity.grid[2].segments.before_step | {'persistent_rotors': 1, 'singularity_count_max': 4, 'singularity_count_mean': 0.48955223880597015, 'singularity_frames_frac': 0.35522388059701493, 'persistent_rotor_count_max': 1, 'persistent_rotor_durations': [{'end': 3045, 'start': 2992, 'charge': -1, 'lifetime_cycles': 1.04, 'lifetime_frames': 54, 'frames_in_segment': 54}], 'persistent_rotor_frames_frac': 0.08059701492537313} | [absent] |
| sensitivity.grid[3].findings.persistent_rotors.before | 1 | 0.11641791044776119 |
| sensitivity.grid[3].findings.persistent_rotors.lifetimes_frames | {'after_step': [], 'before_step': [78]} | [absent] |
| sensitivity.grid[3].findings.persistent_rotors.ratio | [absent] | None |
| sensitivity.grid[3].findings.persistent_rotors_fraction_superseded | {'after': 0.0, 'holds': True, 'label': 'holds (provisional)', 'ratio': None, 'before': 0.11641791044776119} | [absent] |
| sensitivity.grid[3].segments.after_light | [absent] | {'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} |
| sensitivity.grid[3].segments.after_step | {'persistent_rotors': 0, 'singularity_count_max': 4, 'singularity_count_mean': 0.10442477876106195, 'singularity_frames_frac': 0.05929203539823009, 'persistent_rotor_count_max': 0, 'persistent_rotor_durations': [], 'persistent_rotor_frames_frac': 0.0} | [absent] |
| sensitivity.grid[3].segments.before_light | [absent] | {'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} |
| sensitivity.grid[3].segments.before_step | {'persistent_rotors': 1, 'singularity_count_max': 4, 'singularity_count_mean': 0.5716417910447761, 'singularity_frames_frac': 0.4, 'persistent_rotor_count_max': 1, 'persistent_rotor_durations': [{'end': 3126, 'start': 3049, 'charge': -1, 'lifetime_cycles': 1.5, 'lifetime_frames': 78, 'frames_in_segment': 78}], 'persistent_rotor_frames_frac': 0.11641791044776119} | [absent] |
| sensitivity.grid[4].findings.persistent_rotors.before | 1 | 0.11641791044776119 |
| sensitivity.grid[4].findings.persistent_rotors.lifetimes_frames | {'after_step': [], 'before_step': [78]} | [absent] |
| sensitivity.grid[4].findings.persistent_rotors.ratio | [absent] | None |
| sensitivity.grid[4].findings.persistent_rotors_fraction_superseded | {'after': 0.0, 'holds': True, 'label': 'holds (provisional)', 'ratio': None, 'before': 0.11641791044776119} | [absent] |
| sensitivity.grid[4].segments.after_light | [absent] | {'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} |
| sensitivity.grid[4].segments.after_step | {'persistent_rotors': 0, 'singularity_count_max': 4, 'singularity_count_mean': 0.09469026548672567, 'singularity_frames_frac': 0.05663716814159292, 'persistent_rotor_count_max': 0, 'persistent_rotor_durations': [], 'persistent_rotor_frames_frac': 0.0} | [absent] |
| sensitivity.grid[4].segments.before_light | [absent] | {'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} |
| sensitivity.grid[4].segments.before_step | {'persistent_rotors': 1, 'singularity_count_max': 4, 'singularity_count_mean': 0.5656716417910448, 'singularity_frames_frac': 0.3970149253731343, 'persistent_rotor_count_max': 1, 'persistent_rotor_durations': [{'end': 3126, 'start': 3049, 'charge': -1, 'lifetime_cycles': 1.5, 'lifetime_frames': 78, 'frames_in_segment': 78}], 'persistent_rotor_frames_frac': 0.11641791044776119} | [absent] |
| sensitivity.grid[5].findings.persistent_rotors.before | 1 | 0.11492537313432835 |
| sensitivity.grid[5].findings.persistent_rotors.lifetimes_frames | {'after_step': [], 'before_step': [77]} | [absent] |
| sensitivity.grid[5].findings.persistent_rotors.ratio | [absent] | None |
| sensitivity.grid[5].findings.persistent_rotors_fraction_superseded | {'after': 0.0, 'holds': True, 'label': 'holds (provisional)', 'ratio': None, 'before': 0.11492537313432835} | [absent] |
| sensitivity.grid[5].segments.after_light | [absent] | {'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} |
| sensitivity.grid[5].segments.after_step | {'persistent_rotors': 0, 'singularity_count_max': 4, 'singularity_count_mean': 0.07168141592920355, 'singularity_frames_frac': 0.049557522123893805, 'persistent_rotor_count_max': 0, 'persistent_rotor_durations': [], 'persistent_rotor_frames_frac': 0.0} | [absent] |
| sensitivity.grid[5].segments.before_light | [absent] | {'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} |
| sensitivity.grid[5].segments.before_step | {'persistent_rotors': 1, 'singularity_count_max': 4, 'singularity_count_mean': 0.5238805970149254, 'singularity_frames_frac': 0.373134328358209, 'persistent_rotor_count_max': 1, 'persistent_rotor_durations': [{'end': 3125, 'start': 3049, 'charge': -1, 'lifetime_cycles': 1.48, 'lifetime_frames': 77, 'frames_in_segment': 77}], 'persistent_rotor_frames_frac': 0.11492537313432835} | [absent] |
| sensitivity.grid[6].findings.persistent_rotors.before | 1 | 0.20597014925373133 |
| sensitivity.grid[6].findings.persistent_rotors.lifetimes_frames | {'after_step': [], 'before_step': [138]} | [absent] |
| sensitivity.grid[6].findings.persistent_rotors.ratio | [absent] | None |
| sensitivity.grid[6].findings.persistent_rotors_fraction_superseded | {'after': 0.0, 'holds': True, 'label': 'holds (provisional)', 'ratio': None, 'before': 0.20597014925373133} | [absent] |
| sensitivity.grid[6].segments.after_light | [absent] | {'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} |
| sensitivity.grid[6].segments.after_step | {'persistent_rotors': 0, 'singularity_count_max': 7, 'singularity_count_mean': 0.09911504424778761, 'singularity_frames_frac': 0.05398230088495575, 'persistent_rotor_count_max': 0, 'persistent_rotor_durations': [], 'persistent_rotor_frames_frac': 0.0} | [absent] |
| sensitivity.grid[6].segments.before_light | [absent] | {'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} |
| sensitivity.grid[6].segments.before_step | {'persistent_rotors': 1, 'singularity_count_max': 4, 'singularity_count_mean': 0.5283582089552239, 'singularity_frames_frac': 0.39850746268656717, 'persistent_rotor_count_max': 1, 'persistent_rotor_durations': [{'end': 3127, 'start': 2990, 'charge': -1, 'lifetime_cycles': 2.65, 'lifetime_frames': 138, 'frames_in_segment': 138}], 'persistent_rotor_frames_frac': 0.20597014925373133} | [absent] |
| sensitivity.grid[7].findings.persistent_rotors.before | 1 | 0.20597014925373133 |
| sensitivity.grid[7].findings.persistent_rotors.lifetimes_frames | {'after_step': [], 'before_step': [138]} | [absent] |
| sensitivity.grid[7].findings.persistent_rotors.ratio | [absent] | None |
| sensitivity.grid[7].findings.persistent_rotors_fraction_superseded | {'after': 0.0, 'holds': True, 'label': 'holds (provisional)', 'ratio': None, 'before': 0.20597014925373133} | [absent] |
| sensitivity.grid[7].segments.after_light | [absent] | {'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} |
| sensitivity.grid[7].segments.after_step | {'persistent_rotors': 0, 'singularity_count_max': 6, 'singularity_count_mean': 0.09115044247787611, 'singularity_frames_frac': 0.05398230088495575, 'persistent_rotor_count_max': 0, 'persistent_rotor_durations': [], 'persistent_rotor_frames_frac': 0.0} | [absent] |
| sensitivity.grid[7].segments.before_light | [absent] | {'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} |
| sensitivity.grid[7].segments.before_step | {'persistent_rotors': 1, 'singularity_count_max': 4, 'singularity_count_mean': 0.5268656716417911, 'singularity_frames_frac': 0.3970149253731343, 'persistent_rotor_count_max': 1, 'persistent_rotor_durations': [{'end': 3127, 'start': 2990, 'charge': -1, 'lifetime_cycles': 2.65, 'lifetime_frames': 138, 'frames_in_segment': 138}], 'persistent_rotor_frames_frac': 0.20597014925373133} | [absent] |
| sensitivity.grid[8].findings.persistent_rotors.before | 1 | 0.21044776119402986 |
| sensitivity.grid[8].findings.persistent_rotors.lifetimes_frames | {'after_step': [], 'before_step': [141]} | [absent] |
| sensitivity.grid[8].findings.persistent_rotors.ratio | [absent] | None |
| sensitivity.grid[8].findings.persistent_rotors_fraction_superseded | {'after': 0.0, 'holds': True, 'label': 'holds (provisional)', 'ratio': None, 'before': 0.21044776119402986} | [absent] |
| sensitivity.grid[8].segments.after_light | [absent] | {'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} |
| sensitivity.grid[8].segments.after_step | {'persistent_rotors': 0, 'singularity_count_max': 6, 'singularity_count_mean': 0.06991150442477877, 'singularity_frames_frac': 0.04601769911504425, 'persistent_rotor_count_max': 0, 'persistent_rotor_durations': [], 'persistent_rotor_frames_frac': 0.0} | [absent] |
| sensitivity.grid[8].segments.before_light | [absent] | {'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} |
| sensitivity.grid[8].segments.before_step | {'persistent_rotors': 1, 'singularity_count_max': 4, 'singularity_count_mean': 0.4955223880597015, 'singularity_frames_frac': 0.3850746268656716, 'persistent_rotor_count_max': 1, 'persistent_rotor_durations': [{'end': 3130, 'start': 2990, 'charge': -1, 'lifetime_cycles': 2.71, 'lifetime_frames': 141, 'frames_in_segment': 141}], 'persistent_rotor_frames_frac': 0.21044776119402986} | [absent] |
| sensitivity.holds.persistent_rotors_fraction_superseded | False | [absent] |
| sensitivity.trackers[0].finding | [absent] | {'after': 0.0, 'holds': False, 'label': 'does not hold (provisional)', 'ratio': None, 'before': 0.0} |
| sensitivity.trackers[0].findings | {'persistent_rotors': {'after': 0, 'holds': False, 'label': 'does not hold (provisional)', 'before': 0, 'lifetimes_frames': {'after_step': [], 'before_step': []}}, 'persistent_rotors_fraction_superseded': {'after': 0.0, 'holds': False, 'label': 'does not hold (provisional)', 'ratio': None, 'before': 0.0}} | [absent] |
| sensitivity.trackers[0].segments.after_light | [absent] | {'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} |
| sensitivity.trackers[0].segments.after_step | {'persistent_rotors': 0, 'singularity_count_max': 4, 'singularity_count_mean': 0.09469026548672567, 'singularity_frames_frac': 0.05663716814159292, 'persistent_rotor_count_max': 0, 'persistent_rotor_durations': [], 'persistent_rotor_frames_frac': 0.0} | [absent] |
| sensitivity.trackers[0].segments.before_light | [absent] | {'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} |
| sensitivity.trackers[0].segments.before_step | {'persistent_rotors': 0, 'singularity_count_max': 4, 'singularity_count_mean': 0.5656716417910448, 'singularity_frames_frac': 0.3970149253731343, 'persistent_rotor_count_max': 0, 'persistent_rotor_durations': [], 'persistent_rotor_frames_frac': 0.0} | [absent] |
| sensitivity.trackers[1].finding | [absent] | {'after': 0.0, 'holds': True, 'label': 'holds (provisional)', 'ratio': None, 'before': 0.11641791044776119} |
| sensitivity.trackers[1].findings | {'persistent_rotors': {'after': 0, 'holds': True, 'label': 'holds (provisional)', 'before': 1, 'lifetimes_frames': {'after_step': [], 'before_step': [78]}}, 'persistent_rotors_fraction_superseded': {'after': 0.0, 'holds': True, 'label': 'holds (provisional)', 'ratio': None, 'before': 0.11641791044776119}} | [absent] |
| sensitivity.trackers[1].segments.after_light | [absent] | {'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} |
| sensitivity.trackers[1].segments.after_step | {'persistent_rotors': 0, 'singularity_count_max': 4, 'singularity_count_mean': 0.09469026548672567, 'singularity_frames_frac': 0.05663716814159292, 'persistent_rotor_count_max': 0, 'persistent_rotor_durations': [], 'persistent_rotor_frames_frac': 0.0} | [absent] |
| sensitivity.trackers[1].segments.before_light | [absent] | {'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} |
| sensitivity.trackers[1].segments.before_step | {'persistent_rotors': 1, 'singularity_count_max': 4, 'singularity_count_mean': 0.5656716417910448, 'singularity_frames_frac': 0.3970149253731343, 'persistent_rotor_count_max': 1, 'persistent_rotor_durations': [{'end': 3126, 'start': 3049, 'charge': -1, 'lifetime_cycles': 1.5, 'lifetime_frames': 78, 'frames_in_segment': 78}], 'persistent_rotor_frames_frac': 0.11641791044776119} | [absent] |
| sensitivity.trackers[2].finding | [absent] | {'after': 0.0, 'holds': True, 'label': 'holds (provisional)', 'ratio': None, 'before': 0.20298507462686566} |
| sensitivity.trackers[2].findings | {'persistent_rotors': {'after': 0, 'holds': True, 'label': 'holds (provisional)', 'before': 1, 'lifetimes_frames': {'after_step': [], 'before_step': [136]}}, 'persistent_rotors_fraction_superseded': {'after': 0.0, 'holds': True, 'label': 'holds (provisional)', 'ratio': None, 'before': 0.20298507462686566}} | [absent] |
| sensitivity.trackers[2].segments.after_light | [absent] | {'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} |
| sensitivity.trackers[2].segments.after_step | {'persistent_rotors': 0, 'singularity_count_max': 4, 'singularity_count_mean': 0.09469026548672567, 'singularity_frames_frac': 0.05663716814159292, 'persistent_rotor_count_max': 0, 'persistent_rotor_durations': [], 'persistent_rotor_frames_frac': 0.0} | [absent] |
| sensitivity.trackers[2].segments.before_light | [absent] | {'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} |
| sensitivity.trackers[2].segments.before_step | {'persistent_rotors': 1, 'singularity_count_max': 4, 'singularity_count_mean': 0.5656716417910448, 'singularity_frames_frac': 0.3970149253731343, 'persistent_rotor_count_max': 1, 'persistent_rotor_durations': [{'end': 3126, 'start': 2991, 'charge': -1, 'lifetime_cycles': 2.62, 'lifetime_frames': 136, 'frames_in_segment': 136}], 'persistent_rotor_frames_frac': 0.20298507462686566} | [absent] |
| criteria_status.rules | length 13 | length 11 |
| criteria_status.rules[9].description | Baseline step = consensus upward step in tissue-mean raw baseline (cause not inferred; first misread as light onset, contradicted by the DAQ) | Illumination onset = consensus upward step in tissue-mean raw baseline |
| criteria_status.rules[9].expert | optical mapping experimentalist | optogenetics / optical mapping experimentalist |
| criteria_status.rules[9].location | worker/voltage/events.py (detect_baseline_step) | worker/voltage/events.py (detect_illumination_onset) |
| criteria_status.rules[9].values.event_id | 46c59a51-1a01-4aed-8021-db9a63720a1d | 42ba71e2-c2c4-4833-abc2-467506ec90a1 |
| criteria_status.rules[10].description | DAQ channel names from depositor notebook; frames = first N triggers of closest burst; midpoint thresholds | Before/after rotor finding holds if frac(before) >= min_frac and >= min_ratio x frac(after) at every sensitivity level |
| criteria_status.rules[10].expert | experimentalist who recorded the data (or the depositor) | cardiac electrophysiologist + biostatistician |
| criteria_status.rules[10].location | worker/voltage/daq.py | worker/voltage/sensitivity.py (rotor_sensitivity) |
| criteria_status.rules[10].values.files | ['0111210010.txt'] | [absent] |
| criteria_status.rules[10].values.min_frac | [absent] | 0.1 |
| criteria_status.rules[10].values.min_ratio | [absent] | 2.0 |
| pipeline.params.window.illumination | Acquisition log (0111210010.txt, LED trigger channel, provisional interpretation): illumination on throughout the analysed frames 2500-4300. | [absent] |
| pipeline.params.window.illumination_on | [absent] | {'frame': 3170, 'detected': True, 'event_id': '42ba71e2-c2c4-4833-abc2-467506ec90a1', 'uncertainty_frames': 17} |
| pipeline.params.window.segment_cycles_frames.after_light | [absent] | 141 |
| pipeline.params.window.segment_cycles_frames.after_step | 141 | [absent] |
| pipeline.params.window.segment_cycles_frames.before_light | [absent] | 52 |
| pipeline.params.window.segment_cycles_frames.before_step | 52 | [absent] |
| pipeline.params.window.segments.after_light | [absent] | [3170, 4300] |
| pipeline.params.window.segments.after_step | [3170, 4300] | [absent] |
| pipeline.params.window.segments.before_light | [absent] | [2500, 3170] |
| pipeline.params.window.segments.before_step | [2500, 3170] | [absent] |
| pipeline.params.window.split_event | {'kind': 'baseline_step', 'cause': 'not established', 'frame': 3170, 'source': 'image', 'event_id': '46c59a51-1a01-4aed-8021-db9a63720a1d', 'uncertainty_frames': 17} | [absent] |
| 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. Acquisition log (0111210010.txt, LED trigger channel, provisional interpretation): illumination on throughout the analysed frames 2500-4300. Segments were split at a baseline step detected at frame 3170 (+/- 17, source: image, provisional; cause not established): before_step 2500-3170, after_step 3170-4300. Sensitivity: baseline 241, 121, 81 frames x sigma 0.5, 1.0, 2.0 px, and tracker variants. Finding 'singularities in 'before_step' but not (or less in) 'after_step'': across filters holds (provisional). Finding 'persistent rotors in 'before_step' but not (or less in) 'after_step'': across filters holds (provisional); across trackers does not hold (provisional). Finding 'persistent rotors in 'before_step' but not (or less in) 'after_step'': 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. 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. |