Use when
- You need an objective period estimate or a rhythm-strength number for statistics.
- You are comparing rhythm robustness across genotypes or treatments.
- The record is unevenly sampled or has gaps (Lomb-Scargle).
Research Methods
Method
Periodogram analysis for circadian period detection
A periodogram decomposes an activity time series into its rhythmic components and reports the strength of each period, identifying the dominant circadian period and its power. The chi-square (Sokolove-Bushell), Lomb-Scargle, and FFT periodograms, plus cosinor fitting, are the standard tools.
Decision summary
Use a periodogram to turn a continuous activity record into two numbers: the dominant period (free-running period under DD) and its spectral power (rhythm strength). The activity series is tested against a range of candidate periods; the tallest peak near 24 h is the circadian component. Choose the chi-square periodogram (Sokolove-Bushell, with a built-in significance line) or Lomb-Scargle (preferred for uneven or gappy home-cage data) for circadian work, and FFT for long evenly sampled records. Cosinor is a complementary least-squares sinusoid fit, not a periodogram, but is often reported alongside for parametric amplitude and acrophase. Always validate every peak against the actogram.
| Output | Power vs candidate period, with the circadian peak highlighted. |
|---|---|
| Period | Period at the dominant peak (free-running period in DD). |
| Strength | Spectral power at the circadian peak. |
| Significance | Threshold or false-alarm level for the method used. |
Do not use when
- The record is only a few days long, which makes the spectrum unreliable.
- You only need a qualitative picture (use the actogram instead).
Caveats
- Spectral power scales with activity level and record length; compare within a study.
- Detrending and windowing choices change the spectrum.
- Gaps and uneven sampling bias FFT; prefer Lomb-Scargle there.
- A significant peak in a short record can be an artifact.
Reporting checklist
- Method (chi-square, Lomb-Scargle, FFT, cosinor) and software.
- Record length, bin size, and detrending.
- Peak period and peak power, with the significance threshold.
- Lighting condition and activity measure.
References
Sokolove PG, Bushell WN. 1978. The chi square periodogram: its utility for analysis of circadian rhythms.
Original chi-square periodogram for circadian period detection.
https://doi.org/10.1016/0022-5193(78)90022-x
Refinetti R, Cornélissen G, Halberg F. 2007. Procedures for numerical analysis of circadian rhythms.
Comparative review of spectral and periodogram methods.
https://doi.org/10.1080/09291010600903692
Cornelissen G. 2014. Cosinor-based rhythmometry.
Cosinor fitting for mesor, amplitude, and acrophase.
https://doi.org/10.1186/1742-4682-11-16
Related surfaces
Use these related surfaces to move from the scientific method question to the relevant product page, endpoint definition, analysis tool, or adjacent guide.
ConductPhenotype
Runs periodogram and cosinor analysis on home-cage activity.
Actogram (method)
The visual companion to validate periodogram peaks.
Circadian spectral power (endpoint)
The rhythm-strength number the periodogram returns.
Free-running period (endpoint)
The period at the dominant periodogram peak.
