masked_data_RG_80nM run 0ff9236f

masked_data_RG_80nM, run 0ff9236f

Status done, stage done; requested by project lead; worker local worker; started 2026-10-28 15:51 UTC, finished 2026-10-28 15:54 UTC, 198 s; signature 2ed01b48

Stages

Stage	Started	Seconds
claimed	15:50:58	0.2
pipeline_check	15:50:58	25.0
baseline_rule	15:51:23	0.9
deposit_checks	15:51:24	0.5
analysis	15:51:25	26.1
render	15:51:51	169.2
persist	15:54:40	1.8
critic	15:54:42	29.9
done	15:55:12	-30.2

Log

Time	Agent	Action	Detail
15:50:58	web	run queued	{"by": "project lead", "recording_id": "fd37b915-d1c3-42d1-8975-98464215d978", "rerun": true, "run_id": "0ff9236f-c34a-47ba-98dd-89140428ed16"}
15:51:23	runs	run started	{"checked_by": "openai:gpt-5.5", "protocol_params_version": 1, "recording_id": "fd37b915-d1c3-42d1-8975-98464215d978", "run_id": "0ff9236f-c34a-47ba-98dd-89140428ed16"}
15:54:42	runs	signature written	{"criteria": "provisional", "holds": null, "run_id": "0ff9236f-c34a-47ba-98dd-89140428ed16", "signature_id": "2ed01b48-85e8-4e7d-bd5d-fff819580b0c"}

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 v1.

Field	Protocol	Recording	Severity	Detail
no mismatches

Anomaly	Severity	Effect on the Fixed Pipeline
pre-deposit processing	warn	The file is preprocessed rather than raw: the paper documents normalization, 0–100 Hz low-pass filtering, baseline-drift removal and 3-by-3 spatial binning, and the measured flags are consistent with that. The protocol's spatial_sigma 1.0 Gaussian for phase therefore adds filtering on top of prior filtering of known type but unknown exact deposited implementation; noise/SNR and raw-count assumptions should not be interpreted as if the data were raw.
polarity/sign	warn	Measured polarity is non-inverted even though RH237 normally dims on depolarization, so the deposited values appear sign-flipped relative to conventional raw RH237 fluorescence. Because the measured polarity is consistent across all checked blocks, this should not block analysis if the pipeline uses the measured orientation rather than assuming raw RH237 sign.
mask convention	warn	Only frame 0 carries the NaN tissue mask; later frames contain finite non-tissue values. The analysis must use the depositor/measured frame-0 mask and should not define tissue from finite pixels in later frames.
baseline-window rule	info	The coded baseline rule passed: baseline_frames 121 is at least 2.0 times the slowest segment cycle reported by the baseline-rule tool. This is reported only as the code's provisional baseline/cycle check and is not a manual hold criterion.

The recording fits the protocol identity: it is the Zenodo 18319102 rat whole-heart ventricular-fibrillation reference upload, with the on-record/uploaded frame rate of 1000.0 Hz and a pixel size of 112.5 µm, and the protocol does not specify conflicting species, tissue, indicator, frame-rate, pixel-size, or image-size requirements. The fixed version-1 parameters can therefore be run as stated, but interpretation must note that the deposited movie is already normalized, low-pass filtered, baseline-corrected and spatially binned, so the protocol's phase Gaussian is applied to data with prior smoothing and raw-noise/SNR assumptions are not valid. The sign and mask conventions are also non-raw conventions but are internally consistent and do not require holding the run when handled as measured.

Inspector

This is a 128 × 80 rat whole-heart ventricular-fibrillation optical mapping recording associated with rotigaptide 80 nM, with 3800 frames and an on-record frame rate of 1000 Hz from the uploader; the linked paper independently states 1000 frames/s and the same 128 × 80 camera size. Treat it as preprocessed rather than raw: the paper documents 3-by-3 spatial binning, 0–100 Hz low-pass filtering, baseline-drift removal, and normalization, consistent with the measured unit range and strong temporal/spatial smoothing flags. The measured signal polarity is non-inverted, while RH237 would normally dim on depolarization, so the sign appears flipped before deposit but is consistent across all blocks. Use the frame-0 NaN tissue mask, be cautious interpreting SNR because smoothing inflates it, and use the actual 3.8 s duration rather than the paper's generic 10 s recording duration.

Measurement	Value	Method, Caveat
SNR, median (p10–p90)	18.8 (13.9–25.9)	assumes white noise; on temporally smoothed deposits noise is underestimated and SNR inflated
Mask coverage	50.9%, 5216 of 10240 px	depositor NaN mask (frame 0)
Polarity	blocks 7, inverted False, blocks agreeing 7, median dvdt skew 0.08132843673229218	sign of median per-pixel skew of dV/dt, baseline-corrected (121 frames)
Drift / bleaching	baseline change -0.0108, vs beat amplitude -0.0979, slow range 0.162, trend, Spearman -0.356	running median (381 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	unit range, non integer, nan mask partial, temporal smoothing, spatial smoothing	deposit checks
Dominant cycle by block, frames	0–1000: 25.0, 1000–2000: 26.3, 2000–3000: 25.0, 3000–3800: 25.0

Concern	Severity	Detail
pre-deposit processing	warn	The recording is already processed: prior-processing flags show unit-range data [0.0, 1.0], very low integer fraction 0.0003442292944785276, temporal-smoothing metric 0.959237783400513, and spatial-smoothing metric 0.9479694003115444. These are largely explained by the paper's normalization, 0–100 Hz low-pass filtering, and 3-by-3 spatial binning, but analyses that assume raw camera counts or unfiltered noise would be misleading.
polarity/sign	warn	Measured polarity is non-inverted even though RH237 normally dims on depolarization, so the depositor appears to have flipped the sign. Because all 7 of 7 measured blocks agree, this should not make analysis wrong if the pipeline orients polarity from measurement.
mask convention	warn	Only frame 0 has the NaN mask; other frames carry non-tissue values. Downstream analysis must use the measured/depositor mask rather than treating all finite pixels in later frames as tissue.
duration relative to paper methods	info	The linked paper says recordings were 10 seconds long at 1000 frames/s, but this uploaded file has 3800 frames, i.e. 3.8 seconds at the on-record 1000 Hz frame rate. Duration-sensitive analyses should use the actual frame count, not the paper's general acquisition duration.
provisional tool thresholds	info	Conclusions from prior-processing flags, SNR caveats, rhythm detection, and reference-rate machinery depend on provisional thresholds/rates that have not yet been reviewed by a domain scientist. In this case no physiology-inferred frame rate was needed because the uploader and paper state the frame rate.

Inspector report 2026-10-28 15:50 UTC, model openai:gpt-5.5, provisional. Median per-pixel SNR over tissue is 18.818067017408147, with p10 13.893293967898506 and p90 25.936276941781777, using 3000 frames. The SNR tool cautions that temporally smoothed deposits can have underestimated noise and inflated SNR; this recording shows a temporal-smoothing flag. Mask coverage comes from a depositor NaN mask in frame 0: 5216 tissue pixels out of 10240 total pixels, coverage 0.509375, with 5024 NaN pixels in frame 0. No stored events were returned, no acquisition log is present, and no detected light transitions or image baseline-step events were returned. Therefore there are no event causes to assign for this file; in particular, without an acquisition log, no image baseline change could be called illumination. The acquisition-log result explicitly says there is no acquisition log in the deposit. The tissue-mean slow baseline starts at 0.4981755316257477 and ends at 0.48741528391838074, a change of -0.010760247707366943, which is -0.09788043294092134 of the p5–p95 beat amplitude. The slow baseline range is 0.1622154712677002 and the monotonic trend Spearman value is -0.3557674750723145. The drift/bleaching tool cautions that baseline steps, depositor normalization, and drift removal can change or erase the baseline, so bleaching cannot be separated here.

Range checks

Metric	Segment	Value at Run Setting	Cited Range	Status
persistent rotor tracks	all	303 count	none cited	unstable not reportable
dominant freq (Hz)	whole recording	40.29 Hz	none cited	no cited range
persistent rotors	whole recording	303 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	15 count	none cited	unstable not reportable

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