Per-frame F0 baseline rises artificially at the end of each analysis trial

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Issue 类型
缺陷
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基本清楚
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data

调研方向

Start in extractTrial and trace how splitFreq, fitB, and the sources/temporal/F0 baseline are produced. Plot B and the splitFreq low-pass for single pixels near trial ends, as suggested, to identify where the rise begins. Done means the baseline no longer rises artificially at trial ends and F0 behaves consistently across trial edges; the issue gives no test or validation entry point.

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描述

bug

Summary

Source extraction's per-frame baseline (B in extractTrial, reported per source as sources/temporal/F0) rises over the last few seconds of every analysis trial. Over the same frames the raw fluorescence falls, so the rise comes from the baseline fit rather than the data. It also contributes to steps in F0 at trial edges.

Evidence

Dataset: 780125 Neuron1, 2025-03-14 (Z:\ophys\Maedeh\V1_visual_stimuli\780125\slap2_780125_2025-03-14_09-30-06\Neuron1), analysis trials 2–6 (five 28 s trials, about 0.55 s apart), SLAP2, 200 Hz analysis rate.

Method: each source's per-frame F0 was divided by its own median and averaged across sources, with discarded frames excluded. Each trial was then normalized to its own mean and the trials were averaged. global/F (raw whole-field fluorescence) is the reference.

Path2 (dendrites, 68 sources) Path1 (soma plane, 107 sources)
Last 2 s vs. trial middle, F0 +1.2% +2.2%
Last 2 s vs. trial middle, global F −1.0% −3.4%
First 2 s vs. trial middle, F0 +6.8% +4.8%
First 2 s vs. trial middle, global F +3.1% +6.4%
F0 step across the 4 trial edges +4.2, +2.3, +1.9, +1.5% −0.6, −3.5, +0.1, −0.5%
Global F step across the same edges +2.5, +0.3, −0.1, +0.8% −1.9, +1.3, +0.3, +2.0%
  • Trial ends: F0 and raw fluorescence move in opposite directions, so this looks like an artifact.
  • Trial starts: raw fluorescence really is higher (recovery during the gap between trials), but on Path2 F0's start excess is about twice global F's, so F0 likely overshoots there too.
  • Not footprint scale: sources/temporal/F0 = H'B/sum(H.^2) depends on footprint shape, but the median sum(H.^2) is constant across trials, and the footprint-weighted mean of B shows the same pattern.

Likely causes (not yet confirmed)

  • splitFreq interpolates the lower envelope of page means with interp1(..., 'linear', 'extrap'), so the baseline is extrapolated past the last full page. lowess and movmean smoothing are also less constrained at the ends.
  • fitB includes sinePredictors and the surround high-pass terms, which are unconstrained at the trial boundaries.

Suggested next steps

  • Plot B and the splitFreq low-pass for single pixels near trial ends, to see which step introduces the rise.
  • Consider fitting the baseline over padded data (reflect at the edges) or fitting adjacent trials jointly, so the baseline can't diverge at trial edges.

Workaround in progress

The per-trial F0 images being added to per_trial_summary.h5 (per_trial_F0_im) will leave out the first and last few seconds of each trial when averaging. The per-frame F0 traces (sources/temporal/F0) are still affected.

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