Prerau Laboratory — public code catalog

The Prerau Laboratory at Brigham and Women's Hospital / Harvard Medical School develops statistical-signal-processing and machine-learning tools for understanding sleep neurophysiology. This repository is the master index of our public code.

• Website: sleepeeg.org · prerau.bwh.harvard.edu
• Contact: Michael J. Prerau, Ph.D. — prerau@bwh.harvard.edu

Contents

• Core analysis toolboxes
• Paper companion code
• I/O and data tools
• Utilities & infrastructure
• Sleep data / analysis
• How to cite our work

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Core analysis toolboxes

Toolbox	Description	Key reference
multitaper_toolbox	MATLAB, Python, and R implementations of the multitaper spectrogram (optional Rust backend)	Prerau et al., Physiology 2017
DYNAM-O	Dynamic Oscillation Toolbox v1.0 (MATLAB) — TF-peak + SO-power / SO-phase histograms	doi:10.1093/sleep/zsac223
pyDYNAM-O	Python port of DYNAM-O	doi:10.1093/sleep/zsac223
Spindle_dynamics_toolbox	Individualized temporal patterns of human sleep spindle timing	Chen et al., PNAS 2025
Apnea_dynamics_toolbox	Point-process models for respiratory event timing in OSA	doi:10.1093/sleep/zsac189
sleep_onset_modeling	Bayesian particle-filter model of the sleep-onset process	doi:10.1371/journal.pcbi.1003866
MTSleepScoring	Interactive MATLAB GUI for manual sleep-stage scoring on multitaper spectrograms	—
artifact_detection	Iterative z-score artifact detection for continuous time-series data	—
rate_xvalidation	Cross-validated Hanning-kernel point-process firing-rate estimator	doi:10.1152/jn.01036.2010 (Prerau & Eden 2011)
learningcurves	State-space and particle-filter learning-curve estimators	Prerau & Eden 2011
multicomp_test	Permutation and FDR-controlled multiple-comparison tests for 1-D/2-D data	—

Paper companion code

Repositories published alongside a specific paper. Please cite the paper listed.

Repo	Paper
TF_sigma_peaks_SLEEP2021	Dimitrov, He, Stickgold, Prerau. Sleep 2021 — doi:10.1093/sleep/zsab099
IEEE_peak_tracking_paper	Stokes, Prerau. IEEE Access 2020 — doi:10.1109/access.2020.3042737
Spindle_dynamics_toolbox	Chen et al. PNAS 2025 (cross-listed above)
Apnea_dynamics_toolbox	Chen, Redline, Eden, Prerau. Sleep 2022 (cross-listed above)
sleep_onset_modeling	Prerau et al. PLOS Comp Biol 2014 (cross-listed above)
DYNAM-O / pyDYNAM-O	Stokes, Rath, Possidente, He, Purcell, Manoach, Stickgold, Prerau. Sleep 2022 (cross-listed above)

I/O and data tools

Repo	Description
read_EDF	High-performance MEX-accelerated EDF/EDF+ reader for MATLAB
EDF_deidentify_toolbox	Standalone GUI + MATLAB/Python source to de-identify EDF files
data_IO	EDF, BrainVision, MBF, Grass scoring, bytestream, log-file helpers

Utilities & infrastructure

Repo	Description
preraulab_utilities	Meta-repository bundling the nine general-purpose utility sub-repos below
↳ binning	1-D / N-D binning and sliding-window histograms
↳ conversion	Numeric/struct/table/CSV conversion utilities
↳ data_processing	Run-/chunk-/interval-based signal utilities
↳ fig_tools	Figure layout, axes linking, interactive pan/zoom
↳ graphical	Higher-level plot primitives (shaded bounds, Gantt, phase histograms)
↳ nanstats	NaN-aware statistical helpers
↳ read_EDF	EDF/EDF+ reader (cross-listed)
↳ workspace	MATLAB workspace management
↳ CSSuicontrols	CSS-styled HTML-backed UI controls for uifigure apps
EventMarker	Interactive event-marker manager for MATLAB plots
colormaps	Perceptually-uniform and custom colormaps for MATLAB

Sleep data / analysis

Repo	Description
sleep	Sleep EEG analysis toolbox: staging I/O, hypnograms, slow-wave extraction, simulations

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How to cite our work

Each code repository includes a CITATION.cff file. When you use one of our tools in a publication, please cite both (a) the peer-reviewed paper listed in CITATION.cff (under preferred-citation) and (b) the software entry itself. GitHub exposes the citation in the sidebar of every repo — click "Cite this repository" to copy BibTeX or APA.

For general correspondence: prerau@bwh.harvard.edu.