mouse_2609_150ms_control_iDS, run c5f2f922
Status done, stage done; requested by project lead; worker worker; started 2026-10-28 18:19 UTC, finished 2026-10-28 18:36 UTC, 1014 s; signature fb291437
Stages
| Stage | Started | Seconds |
|---|---|---|
| claimed | 18:18:34 | 0.2 |
| inspector | 18:18:34 | 50.1 |
| pipeline_check | 18:19:24 | 24.9 |
| baseline_rule | 18:19:49 | 4.0 |
| deposit_checks | 18:19:53 | 3.3 |
| analysis | 18:19:56 | 836.3 |
| render | 18:33:52 | 97.3 |
| persist | 18:35:29 | 4.2 |
| critic | 18:35:34 | 68.5 |
| done | 18:36:42 | 0.1 |
Log
| Time | Agent | Action | Detail |
|---|---|---|---|
| 18:17:46 | admission | recording registered | {"by": "project lead", "candidate_id": "7764050e-2852-4537-8f72-eb2833c0f619", "deposit": "10.5281/zenodo.5557829", "member": "mouse_2609_150ms_control_iDS.mat", "paper": "10.1371/journal.pone.0259174", "recording_id": "669d42ed-e0bf-4229-9a5f-9301454eafe0", "run_id": "c5f2f922-0262-43d1-a88b-7c3845dcf413", "shape": [1954, 200, 200]} |
| 18:19:49 | runs | run started | {"checked_by": "openai:gpt-5.5", "protocol_params_version": 3, "recording_id": "669d42ed-e0bf-4229-9a5f-9301454eafe0", "run_id": "c5f2f922-0262-43d1-a88b-7c3845dcf413"} |
| 18:35:34 | runs | signature written | {"criteria": "provisional", "holds": null, "run_id": "c5f2f922-0262-43d1-a88b-7c3845dcf413", "signature_id": "fb291437-f9f0-453c-a143-b2d9ffda8720"} |
Entries from the audit log for this run; new rows and stage changes arrive by realtime while the run is open (connecting).
Pipeline check
Proceed: True; parameters v3.
| Field | Protocol | Recording | Severity | Detail |
|---|---|---|---|---|
| no mismatches | ||||
| Anomaly | Severity | Effect on the Fixed Pipeline |
|---|---|---|
| Undocumented pre-deposit transformation | warn | The deposited movie contains all-negative integer values rather than raw non-negative fluorescence counts, so amplitude offsets, sign, and any prior normalization or subtraction are not documented. The fixed pipeline can still run, but voltage scale and baseline-sensitive interpretations should be treated cautiously. |
| Polarity confidence | warn | The measured orientation is non-inverted but low-confidence, so the pipeline should rely on its measurement-based orientation rather than dye expectation. Phase/activation conclusions that depend on polarity are less secure. |
| Whole-frame mask | warn | Because no depositor mask or NaN tissue mask is present, the whole 200 x 200 frame is treated as tissue by the available mask; background may enter spatial filtering, phase, and rotor analyses unless a better mask is checked or supplied. |
| baseline-window rule | info | The coded baseline rule reports ok for the protocol baseline: baseline_frames 901, factor 2.0, slowest_segment whole_recording, slowest_cycle_frames 15, required_min_frames 30, ratio 60.067. This is reported as informational only and does not determine a hold here. |
The fixed protocol is applicable as a provisional mouse whole-heart optical-mapping analysis because the recording is identified as a mouse whole-heart iDS recording and no recording fact conflicts with the protocol fields; the protocol does not specify an indicator, frame rate, pixel size, or image size that would be contradicted. The admitted frame rate is 977.0 Hz from the paper methods, and the coded baseline-window rule passes for the available segment. The main limitations are not protocol mismatches but data-quality and provenance warnings: the deposited values appear transformed before deposit, polarity is low-confidence, and the available mask covers the whole frame, so results should be interpreted with those caveats rather than held.
Inspector
This is a mouse whole-heart iDS optical mapping recording with 1954 frames of 200 x 200 pixels; the admitted frame rate is 977.0 Hz and the linked paper independently states 200x200 at 977 FPS. The file is not raw non-negative fluorescence: all values are negative integers, and the deposit does not explain that transformation, although the paper documents conditioning used for analysis. The measured polarity is non-inverted but low-confidence; Di-4-ANEPPS normally dims on depolarization, so rely on measurement-based orientation rather than dye expectation. No acquisition log or stored/detected events are available, and the whole-frame mask should be replaced or checked before spatial analysis.
| Measurement | Value | Method, Caveat |
|---|---|---|
| SNR, median (p10–p90) | 3.8 (3.5–4.1) | assumes white noise; on temporally smoothed deposits noise is underestimated and SNR inflated |
| Mask coverage | 100.0%, 40000 of 40000 px | nonzero temporal std only (no NaN mask in deposit) |
| Polarity | blocks 3, inverted False, blocks agreeing 2, median dvdt skew 2.585476977401413e-05 | sign of median per-pixel skew of dV/dt, baseline-corrected (121 frames) |
| Drift / bleaching | baseline change 28.5, vs beat amplitude 0.596, slow range 1.53e+03, trend, Spearman 0.474 | running median (195 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 | deposit checks |
| Dominant cycle by block, frames | 0–1000: 142.9, 1000–1954: 95.4 |
| Concern | Severity | Detail |
|---|---|---|
| Undocumented pre-deposit transformation | warn | prior_processing flags processed_before_deposit=true solely from negative_values: min -7378.0, max -4.0, negative_frac 1.0, integer_frac 1.0. Raw fluorescence counts should be non-negative, and neither Zenodo metadata nor paper text explains the all-negative values in this deposited file. |
| Polarity confidence | warn | Measured polarity is inverted=false, but median_dvdt_skew is very small (0.00002585476977401413) and only 2 of 3 blocks agree; use pipeline measurement-based orientation rather than assuming raw Di-4-ANEPPS fluorescence polarity. |
| Whole-frame mask | warn | Mask coverage is 1.0 because no NaN/depositor mask exists and the mask is based only on nonzero temporal standard deviation; background may be analyzed as tissue unless a better mask is made. |
| SNR and processing thresholds are provisional | info | SNR and the flags used to infer prior processing come from provisional tool thresholds/methods, and the SNR caveat says temporal smoothing would inflate SNR. |
Inspector report 2026-10-28 18:19 UTC, model openai:gpt-5.5, provisional. Median per-pixel SNR over tissue is 3.84442891322745, with p10 3.5463776973489423 and p90 4.104365003976118, using all 1954 frames. The SNR method assumes white noise; if temporally smoothed before deposit, noise may be underestimated and SNR inflated. The mask includes 40000 tissue pixels out of 40000 total pixels, coverage 1.0, with 0 NaN pixels in frame 0. The mask comes only from nonzero temporal standard deviation, not from a depositor-provided NaN/tissue mask, so it may include background. No stored events were returned, the acquisition_log tool reports no acquisition log in the deposit, and detected_events returned no events. Therefore there are no logged light transitions or image baseline steps to label for this recording; in particular, there is no evidence from an acquisition log for any illumination change during the recording. The running-median tissue mean changes from -3064.182861328125 to -3035.669921875, a baseline_change of 28.512939453125, which is 0.5963059756456527 times the p5-p95 beat amplitude of 47.81595458984375. The slow_baseline_range is 1533.4964599609375 and the last slow-baseline sample jumps to -1532.091; the tool cautions that steps, normalization, or drift removal can change/erase baseline, so bleaching cannot be separated here.
Range checks
| Metric | Segment | Value at Run Setting | Cited Range | Status |
|---|---|---|---|---|
| persistent rotor tracks | all | 1104 count | none cited | unstable not reportable |
| dominant freq (Hz) | whole recording | 7.169 Hz | none cited | unstable not reportable |
| persistent rotors | whole recording | 1104 count | none cited | unstable not reportable |
| singularity frames fraction | whole recording | 1 fraction of frames | none cited | no cited range |
| persistent rotor count max | whole recording | 51 count | none cited | unstable not reportable |
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