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SDR-0003: Represent subtraction and division as different transformations

  • Status: Accepted
  • Date: 2026-07-26
  • Decision owners: project maintainers
  • Related protocol/report: protocol v0.2, report v0.2

Context

Bleaching can affect indicator fluorescence, additive autofluorescence, or both. Division assumes the estimated baseline scales physiological amplitude and yields a fractional dF/F quantity. Subtraction assumes an additive baseline and retains acquired-fluorescence units. Calling both outputs dF/F would conceal incompatible generative assumptions.

The frozen v0.2 simulation found that division preserved early-to-late response amplitude under indicator bleaching (-0.2% change), while subtraction attenuated it by 25.9%. Under additive autofluorescence bleaching, subtraction was stable (-0.4%) while division inflated late responses by 34.4%.

Decision

Require callers to choose divide or subtract. Divisive output is named dff; subtractive output is named baseline_subtracted and remains in acquired fluorescence units. Store the choice and formula in provenance. Do not silently normalize a subtractive result afterward or present either choice as universally correct.

Consequences

Downstream pipelines must acknowledge the transformation and cannot accidentally pool unlike units. Users need biological or acquisition evidence to choose. Some existing tools use “dF/F” more loosely, so interoperability documentation must make the semantic difference explicit.

Alternatives considered

  • Always divide: rejected because additive autofluorescence creates time-varying fractional scaling.
  • Always subtract: rejected because indicator bleaching attenuates physiological amplitude in acquired units.
  • Return both under generic names: rejected because it encourages opportunistic selection and unit confusion.

Revisit trigger

Revisit if an independently validated generative model can estimate indicator and autofluorescence components jointly, or if acquisition metadata provides those components directly.

Evidence added later

None.