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Fear Conditioning Analyzer

Analyze cued freezing, contextual freezing, and conditioning-minus-neutral generalisation from animal-level fear conditioning scores.

Cued FreezingContextual FreezingCSV Export
AnimalGrouppre_CS_%CS_%post_CS_%shock_mA

Cued freezing summary

CS minus pre-CS freezing

Animal deltas

M1 (vehicle)56.0%
M2 (vehicle)50.0%
M3 (drug)31.0%
  • Compute cued freezing as CS percent minus pre-CS baseline percent
  • Summarize contextual freezing in the conditioning context
  • Estimate context generalisation from conditioning and neutral contexts
  • Compare treatment or genotype groups with mean and SEM charts
  • Export animal-level cued and contextual summaries

Don't use for

  • Velocity-trace freezing detection from raw video or tracker output
  • Extinction curves with repeated CS bins across sessions
  • Fear-potentiated startle, which uses startle amplitude rather than freezing

Resources

  • Tone duration and frequency documented
  • Shock magnitude and duration documented
  • Pairing count fixed before analysis
  • Pre-CS baseline reviewed before cued scoring
  • Context A and context B differences documented
  • Locomotor or sedation confounds checked
  • Freezing detection threshold validated

What Is Fear Conditioning?

Fear conditioning is a Pavlovian learning paradigm in which a neutral cue or context becomes associated with an aversive event. In rodent studies, the unconditioned stimulus is usually a brief mild foot shock, and the behavioral readout is percent time freezing.

A complete analysis usually separates cued fear from contextual fear. Cued freezing asks whether the animal freezes more during the tone than before the tone. Contextual freezing asks whether the animal freezes in the conditioning chamber when no tone or shock is presented.

Metrics and Math

Cued freezing is computed as CS freezing percent minus pre-CS baseline freezing percent. Contextual freezing is reported as the raw percent freezing in the conditioning context. Generalisation index is conditioning-context freezing percent minus neutral-context freezing percent.

Group charts summarize animal-level values as mean +/- SEM. The tool does not run hypothesis tests because factorial designs, repeated CS trials, sex, drug dose, and batch effects usually need a planned statistical model.

Best Practices

Report tone duration, shock intensity, shock duration, pairing count, inter-trial intervals, context A and context B differences, and freezing detection criteria. Keep baseline freezing low in the cued test by making the neutral context truly distinct.

Review locomotor activity if a treatment changes freezing. Drugs that reduce movement can inflate apparent freezing even when associative fear learning is unchanged.

Frequently Asked Questions

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