Fiber photometry of the suprachiasmatic nucleus — the brain's master clock — recorded continuously for 14–17 days in constant darkness, with wheel-running behavior and a single light pulse that resets the clock mid-record.
Calcium-dependent fluorescence (ΔF/F₀, 470 nm signal / 415 nm isosbestic correction) alongside wheel revolutions, across the entire recording. The shaded band is the min–max envelope per 6-minute bin; the line is the running signal. The gold line marks the light pulse.
Zeitgeber time is cumulative from recording start (ZT0 = lights-on convention of the prior LD cycle; in DD it free-runs). ΔF/F₀ baseline = mean of ZT14–22 on cycle 1, per the lab's MATLAB pipeline.
The classic circadian biology view: each row is one day, hours left→right. Darker = more wheel running. In constant darkness a healthy clock free-runs with τ slightly under 24 h, so activity onsets drift left. After the light pulse (gold row marker) the rhythm shifts — that's phase resetting, the SCN doing its job.
Zoomed to ±12 h around the pulse (15-second resolution). This is photic phase resetting in action: a 30-min light pulse in the behavioral night acutely suppresses then releases SCN calcium, and the clock's phase is rewritten for the days that follow.
Pre/post periods below come from a χ² periodogram (Sokolove–Bushell) on wheel activity before vs. after the pulse. In DD, mice run ~23.3–23.6 h cycles — shorter than 24 h, as expected for the species.
Each animal carries two measurable oscillators: when it starts running (the wheel clock) and when SCN calcium reaches its daily minimum (the calcium clock). The light pulse rewrites both — but not identically, and the disagreements are the interesting part.
| Animal | Full shift | LOO range | Read |
|---|
Shift = pre/post-pulse regression difference at the pulse cycle, in circadian hours (×24/τ pre). Calcium clock anchored on the daily ΔF/F minimum (CT18, night trough).
Correlation between the two clocks' shifts: — — no reliable coupling at this sample size; a lead, not a conclusion. An earlier calcium-shift estimator (ΔF-weighted circular mean) produced r = −0.93; the corrected daily-minimum anchor flips two animals' calcium signs and gives the value shown. 6978's advance is confirmed by its calcium clock (+3.4 CT) — its noisy wheel data had underestimated it — while 7390's wheel-clock advance (+4.3 CT) vanishes in the calcium frame (−0.8): its wheel onsets drove that outlier. Flag: 7390 runs in the opposite absolute-ZT half from the four 221014 animals (83% of wheel events in ZT0–12 vs 4–29% for the others), consistent with a ~12 h difference in session ZT convention or release phase — within-animal CT analyses are unaffected; cross-session absolute-ZT comparisons are not.
Two independent noise models — a 24-h sine fit and a circadian signal-to-noise ratio — screened all ten recordings before any physiology was interpreted. Five animals survived; the keep/exclude calls were then reviewed by the researcher who collected the data.
| Animal | Genotype | Sensor | Circadian SNR | Sine amplitude (z) | R² | Model verdict | Final |
|---|
GFP animals are fluorescence controls — their ΔF/F is movement artifact, not biology. 6577 is statistically borderline (SNR 0.65) but was kept after review: it shows a clear rhythm. 7121/7122 (GFlamp1) carry no detectable signal; 7381's fiber was likely off-target.
Three questions asked of the wheel data: does a heavy night buy a quieter following day (the mice could be sleeping more soundly)? Does more running change the next cycle's length? And do the light shifts at recording start contaminate the first days?
Per circadian cycle, wheel clock. No compensation: heavy nights do not buy detectably quieter days in this cohort.
Dividing revolutions by window length suggests a strong negative activity→period effect (pooled r = −0.41, p = 0.001) — but the window is the outcome variable. Permuting counts while keeping windows (structural null) reproduces most of it. Honest verdict: no per-cycle activity feedback detectable here.
Dropping the first 1–3 days (light-shift transient at recording start) does not shrink the two large advances — if anything it grows them. But the pre-pulse onset count shrinks with each skip (7390: 6 → 3), so the growing values increasingly rest on thin fits. The sign of every animal's conclusion is stable; magnitudes beyond skip-1 are fragile.
When a mouse breaks a ≥10-min stillness and starts running, SCN calcium rises. The size of that rise depends on circadian time — and the pattern differs between animals.
CT frame from wheel onsets (onset = CT12); bins 12–18 and 18–24 are the subjective night. 6977 and 6978 show the early-night > late-night gradient; 7390 doesn't; VIP 6976 runs flat — the odd one out.
Baseline-normalized (mean of −60…−10 s → 0). Shading = SEM across animals.
Splitting bout onsets by early (CT12–18) vs late (CT18–24) night gives the curves below. In bulk ΔF/F, VIP-Cre and D1-Cre animals share the same day-high profile: full-record day/night calcium ratio 1.04–1.14 in the wheel-CT frame, and a cycle-1 LD orientation test of 1.13–1.86 (day-high) in all five animals. The night-firing VIP⁺ subgroup reported in single-unit work is not resolvable in bulk fiber signal — that needs single-cell resolution.
Ten animals across two sessions. D1-Cre and VIP-Cre drivers target distinct SCN-relevant cell populations; GCaMP6s reports calcium, GFlamp1 is a faster green indicator, and GFP animals are the fluorescence control — any "signal" there is movement artifact, not biology.
| Animal | Session | Genotype | Sensor | Sex | Record | τ pre | τ post | Δτ | ΔF/F range |
|---|
τ = free-running period from χ² periodogram (20–28 h window). Δτ = post-pulse minus pre-pulse period. GFP rows are controls; interpret their ΔF/F as artifact, not neural signal.
Everything on this page is computed by a Python port of the lab's MATLAB pipeline, checked against the lab's own MATLAB outputs to numerical exactness before being shown.
loading validation result…
Acquisition. Neurophotometrics 3-color fiber photometry: 470 nm (GCaMP/GFlamp1/GFP excitation), 415 nm (isosbestic control), 560 nm (tdTomato reference). LED states are frame-multiplexed in a single raw CSV stream; channels are demultiplexed on the 0.0039 trigger edge as in the lab's ProcessPhotometryAndWheelData.m.
Correction. Signal = 470/415 (divide-by-isosbestic for all animals here), 30-s centered median filter, ΔF/F₀ with F₀ = mean over ZT 14–22 of the first cycle. Wheel events (ZT-hour timestamps of revolutions) are histogrammed into 10-min bins.
Port validation. The Python demux was compared sample-for-sample against the MATLAB FullTrace.mat outputs: raw channels matched to ~1e-16, corrected signal r = 0.9998, ΔF/F r = 1.0000 (max abs diff ≈ 1.4e-6) on the pilot animal; the cross-session check runs live below against a second-session animal.
Circadian metrics. χ² periodogram (Sokolove & Bushell 1978) on 10-min wheel histograms, 20–28 h period window, computed separately pre/post light pulse.
This is a data exploration dashboard over two exemplar sessions (2022-10-14, n=4; 2022-11-28, n=6) pulled from a 1.5-year, 1.23 TB archive — not a full-cohort study. Trace sections are descriptive; the analysis sections (04–07) report small-sample statistics with permutation tests and explicit fragility flags — n is 5 animals, so treat every correlation as a lead, not a conclusion. Session 221014 contains VIP-Cre and D1-Cre animals (recording quality permitting); 221128 is D1-Cre only, with sensor-type contrasts (GCaMP6s / GFlamp1 / GFP control).
Raw recordings remain on the lab's Dropbox; this page ships only downsampled derived traces (~2 MB).