mouse_2609_150ms_control_MiCAM, run 6e21b7f8
Status done, stage done; requested by project lead; worker worker; started 2026-10-28 18:15 UTC, finished 2026-10-28 18:18 UTC, 186 s; signature 804ddd67
Stages
| Stage | Started | Seconds |
|---|---|---|
| claimed | 18:14:05 | 0.1 |
| inspector | 18:14:05 | 58.2 |
| pipeline_check | 18:15:04 | 23.8 |
| baseline_rule | 18:15:27 | 1.3 |
| deposit_checks | 18:15:29 | 0.8 |
| analysis | 18:15:29 | 41.0 |
| render | 18:16:10 | 75.7 |
| persist | 18:17:26 | 4.0 |
| critic | 18:17:30 | 62.6 |
| done | 18:18:33 | 0.5 |
Log
| Time | Agent | Action | Detail |
|---|---|---|---|
| 18:14:01 | admission | recording registered | {"by": "project lead", "candidate_id": "7764050e-2852-4537-8f72-eb2833c0f619", "deposit": "10.5281/zenodo.5557829", "member": "mouse_2609_150ms_control_MiCAM.mat", "paper": "10.1371/journal.pone.0259174", "recording_id": "ae77081e-a125-471f-8805-27dad0688848", "run_id": "6e21b7f8-7cd1-499c-8e8f-ab37b36c7113", "shape": [2047, 100, 100]} |
| 18:15:27 | runs | run started | {"checked_by": "openai:gpt-5.5", "protocol_params_version": 3, "recording_id": "ae77081e-a125-471f-8805-27dad0688848", "run_id": "6e21b7f8-7cd1-499c-8e8f-ab37b36c7113"} |
| 18:17:30 | runs | signature written | {"criteria": "provisional", "holds": null, "run_id": "6e21b7f8-7cd1-499c-8e8f-ab37b36c7113", "signature_id": "804ddd67-f7b9-45c6-a823-bef795065584"} |
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 |
|---|---|---|
| Frame-rate provenance for a MiCAM file | warn | The fixed pipeline can run with the admitted working frame rate of 977.0 Hz, but the provenance is indirect for this MiCAM, 100x100 deposited file because the cited paper statement is for the custom iDS system and 200x200 acquisition. Time-based interpretation should therefore cite this caveat. |
| Pre-deposit sign/conditioning | warn | The deposited signal appears non-inverted despite the paper naming Di-4-ANEPPS, which normally dims on depolarization. The downstream pipeline orients recordings from the measurement, so this does not by itself invalidate analysis, but polarity and any sign-dependent interpretation should be treated as pre-conditioned before deposit. |
| Unexplained all-negative data values | warn | All sampled values are negative integers, suggesting baseline subtraction, normalization, or another file-level transformation before deposit. This means amplitude baselines and noise estimates may not reflect raw fluorescence counts, and the protocol's analysis is applied to a processed deposited array. |
| Mask is not a heart segmentation | warn | The analysis mask covers nearly the whole image and is based only on nonzero temporal standard deviation, not a biological heart segmentation. Spatial maps from the fixed pipeline may include non-tissue/background pixels unless a biological mask is generated for interpretation outside this run. |
| Rhythm detector not suitable for the expected paced period here | info | The short dominant cycles reported by rhythm tools should not be used as physiology or for frame-rate inference because the expected paced period from the file label and paper is outside the rhythm tool's baseline-correction window; this is a reporting caveat and not a hold condition. |
| baseline-window rule | info | The coded baseline-window rule passed: baseline_frames 901 is at least 2.0 times the slowest coded cycle, with ratio 128.714. Per policy this rule is reported only as informational and does not change proceed status here. |
The recording may be analysed under the fixed provisional mouse whole-heart protocol as it stands. The protocol does not specify a conflicting fixed indicator, pixel size, frame rate, or image size, and the admitted 977.0 Hz frame rate is the working value on record for this file, although its MiCAM-specific provenance is only medium confidence. The main limitations are not parameter mismatches but provenance and preprocessing warnings: the deposited array appears sign/conditioning transformed, all-negative, and masked nearly as the full image, so the fixed parameters can be applied but results must be interpreted as applying to the processed deposited recording rather than raw fluorescence or a tissue-only mask.
Inspector
This is a mouse whole-heart MiCAM optical-mapping recording from the Zenodo deposit for the open-source low-cost cardiac optical mapping system paper. Use 977.0 Hz because it is already on the recording row from admission, but note that the supporting paper quote is for 200x200 iDS acquisition while this file is 100x100 MiCAM; the observed 142.9-frame cycle is nevertheless consistent with a ~150 ms paced recording at 977 Hz. The deposited signal is not inverted by measurement—depolarization increases values—although Di-4-ANEPPS normally dims on depolarization, suggesting a pre-deposit sign flip or similar transformation. No acquisition log or detected events are available; the file also appears preprocessed/converted because all values are negative, and that specific transformation is not documented in the deposit metadata.
| Measurement | Value | Method, Caveat |
|---|---|---|
| SNR, median (p10–p90) | 15.3 (11.2–20.0) | assumes white noise; on temporally smoothed deposits noise is underestimated and SNR inflated |
| Mask coverage | 11.1%, 1114 of 10000 px | file_variable |
| Polarity | blocks 4, inverted False, blocks agreeing 4, median dvdt skew 0.9510276913642883 | sign of median per-pixel skew of dV/dt, baseline-corrected (121 frames) |
| Drift / bleaching | baseline change 29.6, vs beat amplitude 0.326, slow range 58.9, trend, Spearman 0.394 | running median (205 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, 1000–2000: 142.9 |
| Concern | Severity | Detail |
|---|---|---|
| Frame-rate provenance for MiCAM file | warn | The on-record frame rate is 977.0 Hz from an admission entry quoting the paper, but the quote describes custom iDS software at 200x200 pixels, whereas this recording is a 100x100 MiCAM file. The 977 Hz value is still preferred by the required source hierarchy, and the 142.9-frame rhythm is consistent with the file label/protocol at 150 ms, but the camera/resolution mismatch should be noted. |
| Undocumented pre-deposit processing/sign convention | warn | All sampled values are negative (negative_frac 1.0; min -13413.0, max -25.0), so the file is not raw non-negative camera counts. The deposit metadata does not document the transformation for this file; measured polarity is nevertheless consistent across blocks, so the pipeline can orient it from measurement. |
| Provisional rhythm/rate references | info | The detected dominant cycle is 142.9 frames in both 1000-frame blocks; conclusions using tool reference rates or thresholds depend on provisional, not yet domain-reviewed, criteria. |
Inspector report 2026-10-28 19:16 UTC, model openai:gpt-5.5, provisional. Median per-pixel SNR over the tissue mask is 15.2519519217203, with p10 11.175782496478845 and p90 20.043913618322257 over 2047 frames. The SNR method assumes white noise; if the deposit was temporally smoothed, noise would be underestimated and SNR inflated. The tissue mask contains 1114 pixels out of 10000, coverage 0.1114. It was derived from the file variable bgimage using an Otsu threshold of 2165.203125 and the largest connected component in the class with more temporal signal; there were 0 NaN pixels in frame 0. No acquisition log is present in the deposit, and the stored_events and detected_events tools returned no events for this recording. Therefore there are no logged light transitions or detected image baseline steps to interpret; any pacing interpretation comes only from the label/protocol, not from event detections. The tissue-mean slow baseline changed from -4082.009765625 to -4052.447998046875, a change of 29.561767578125, equal to 0.3261039352774519 of the beat amplitude; the slow baseline range was 58.898681640625 with Spearman trend 0.39378869681589407. The tool cautions that baseline steps, depositor normalization, or drift removal can alter this estimate, and bleaching cannot be separated here.
Range checks
| Metric | Segment | Value at Run Setting | Cited Range | Status |
|---|---|---|---|---|
| persistent rotor tracks | all | 1118 count | none cited | unstable not reportable |
| dominant freq (Hz) | whole recording | 55.99 Hz | none cited | unstable not reportable |
| persistent rotors | whole recording | 1118 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 | 43 count | none cited | unstable not reportable |
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