README.md

metadata

license: cc0-1.0
tags:
  - eeg
  - sleep-staging
  - in-ear-eeg
  - scalp-eeg
  - hdf5

EESM23-Processed

Processed HDF5 export of the EESM23 OpenNeuro dataset. It contains paired in-ear EEG and scalp EEG sleep-staging samples from the scored ses-001 and ses-002 recordings of 10 subjects.

Update: this export now stores one 30-second epoch per sample (previously seven 4-second windows). This matches EESM19-Processed and the canonical sleep-staging unit. See "Preprocessing" below.

Preprocessing

Generated with Ear-EEG-FM-Benchmark/dataset/preprocess_eesm23.py using schema/eegfm version 0.5.0:

• 0.1–100 Hz band-pass and 50 Hz notch filtering on each continuous recording
• no re-referencing, resampling, or channel renaming
• each labeled 30-second AASM scoring event is stored as one 30-second window (one sample = one epoch = one label = one prediction — the canonical sleep-staging unit)
• classes: Wake, N1, N2, N3, REM; Artefact events are dropped
• real sensor/data-loss NaN/Inf samples are preserved and recorded in overall and per-channel quality fields
• the ear-EEG and scalp outputs are strictly row-aligned; a session is excluded from both when either modality is missing/unreadable, and a sample is retained only when it exists in both modalities
• recording bounds are checked per 30-second window (the full epoch must lie inside the recording)
• all signal values are stored as float32 microvolts at 250 Hz (7,500 samples per window)

Brief device data-loss gaps are interpolated before filtering to prevent FIR-kernel contamination, after which the original NaN positions are restored before window selection.

Why 30-second windows (and how to get 4-second windows)

The 30-second epoch is the unit at which sleep is scored (AASM) and evaluated. Every reference EEG foundation model that does sleep (BENDR, EEGPT, CBraMod, REVE, and the EEGPT comparison implementations of LaBraM/BIOT) ingests the full 30-second epoch downstream and emits one stage prediction per epoch, rather than splitting one label into independently-scored short windows. Storing 30 s is also a strict superset: the benchmark loader (dataset/loader.py) accepts an epoch_sec argument and crops a shorter window from each stored sample at load time, so a 4-second (or any ≤30 s) view is available without re-exporting; the reverse is not possible.

Files

File	Channels	Shape (N, C, T)	Size
eesm23-in-ear-eeg.h5	RB, RT, LB, LT	(15,523, 4, 7500)	1.74 GiB
eesm23-scalp-eeg.h5	M1, F3, C3, O1, M2, F4, C4, O2	(15,523, 8, 7500)	3.48 GiB

T = 7500 is one 30-second epoch at 250 Hz. N is the number of scored epochs, one sample per 30-second AASM epoch.

Label distribution (identical for both modalities — the samples are row-aligned):

Wake	N1	N2	N3	REM
1,375	1,292	7,328	2,494	3,034

Retained and discarded epochs

The source scoring files label 17,074 30-second epochs across the 20 sessions (10 subjects × ses-001/ses-002): 16,558 carry one of the five retained sleep-stage labels and 516 are labeled Artefact. Each retained epoch becomes one 30-second sample, so the final files contain 15,523 strictly paired samples per modality. The exclusions from the 16,558 five-class candidates are:

Reason	Epochs
Entire sub-006/ses-002 pair: truncated/unreadable PSG	1,031
30-second epoch out of bounds or with no cross-modality partner	4
Total excluded	1,035

(The 516 Artefact epochs are outside the five-class task and are never candidates.)

sub-006/ses-002 is dropped because its scalp PSG file is truncated/unreadable (OSError: could not read bytes). No sample is excluded because it contains NaN/Inf: the files retain 2,230 in-ear and 1,913 scalp samples with at least one non-finite value; their indices remain paired even when quality differs between modalities.

HDF5 schema (v0.5)

/data                 (N, C, 7500) float32
/durations            (N,)         int64
/nan_fraction         (N,)         float32
/channel_nan_fraction (N, C)       float32
/labels               (N,)         int64
/sample_id            (N,)         int64
/subject              (N,)         string
/session              (N,)         string
/task                 (N,)         string
/acquisition          (N,)         string
/run                   (N,)         string
/recording_id          (N,)         string
/trial_id              (N,)         int64
/event_id              (N,)         int64
/split_group_id        (N,)         int64
/window_start_sample   (N,)         int64
/window_stop_sample    (N,)         int64
/ch_names              (C,)         string

event_id and split_group_id both identify the source 30-second scoring row; here each sample is one epoch, so there is one sample per split group. For sequence-model sleep staging that needs adjacent-epoch context, group by subject+session and order by window_start_sample.

Important attributes include sfreq, class_names, unit, eegfm_version, preprocess_config_json, split_group_kind, and window_reference.

Derived stores

Re-referenced / cleaned / resampled copies of the native stores, built by scripts/sbatch/build_stores.sbatch of github.com/zhikaili1150/Ear-EEG-FM-Benchmark (order: native [-> dataset/reject_electrodes.py] -> dataset/referencing.py -> dataset/make_200hz.py; file-name suffix order = processing order). Full sha256 in SHA256SUMS.

file	rows	bytes	sha256	attrs	code commit	uploaded
eesm23-in-ear-eeg-car-200hz.h5	15523	1496508180	3eccf2acc3f1b6ad…	derived_by=dataset/make_200hz.py; derived_from=data/EESM23-Processed/eesm23-in-ear-eeg-car.h5; derived_src_sfreq=250.0; eegfm_version=0.5.0; reference_scheme=common_average_reference_over_file_channels; sfreq=200.0	11a951ef91	2026-10-06
eesm23-in-ear-eeg-car.h5	15523	1869240088	90af29b0b5d749e1…	derived_by=dataset/make_car.py; derived_from=data/EESM23-Processed/eesm23-in-ear-eeg.h5; eegfm_version=0.5.0; reference_scheme=common_average_reference_over_file_channels; sfreq=250.0	11a951ef91	2026-10-06
eesm23-scalp-eeg-car-200hz.h5	15523	2986964612	b848180225d876c1…	derived_by=dataset/make_200hz.py; derived_from=data/EESM23-Processed/eesm23-scalp-eeg-car.h5; derived_src_sfreq=250.0; eegfm_version=0.5.0; reference_scheme=common_average_reference_over_file_channels; sfreq=200.0	11a951ef91	2026-10-06
eesm23-scalp-eeg-car.h5	15523	3732262232	fe7f889316baf810…	derived_by=dataset/make_car.py; derived_from=data/EESM23-Processed/eesm23-scalp-eeg.h5; eegfm_version=0.5.0; reference_scheme=common_average_reference_over_file_channels; sfreq=250.0	11a951ef91	2026-10-06