Load LFP Features

This guide covers downloading and loading the full-recording compressed LFP archives (release v04) produced by lfpack: lossy HDF5 encodings of the entire LFP trace for every insertion (1099 PIDs), at three tiers. See the lfpack documentation for the reader API.

Note

Reading v04 (lfpack format 2) requires lfpack ≥ 1.0.0 (uv pip install -U "lfpack>=1.0.0"). The v03 archives and the mild / aggressive levels are deprecated and removed; mild → small.

Tiers

All tiers use the same codec (ε = 100); they differ only in α, the wavelet-packet threshold, which is the only parameter that moves decoding.

`level`	α	File	Size	File / float32 at 250 Hz
`small`	14	`lf_compressed_v04_a14_small_all.h5`	11.2 GB	0.57 %
`default`	7	`lf_compressed_v04_a07_default_all.h5`	21.5 GB	1.10 %
`fine`	2.5	`lf_compressed_v04_a2p5_fine_all.h5`	46.1 GB	2.35 %

Use default unless size matters (small, which decodes like the former v03 mild at a third of the size) or fidelity matters (fine).

Every recording carries brain locations (ml/ap/dv/atlas_id/acronym), sync knots, bad-channel labels and the saturation table.

Known exceptions: PID bf96f6d6 has no bad-channel labels, and two PIDs are fully flagged bad and decode to zeros (lfpack#21).

S3 Layout

aggregates/atlas/projects/{project}/
│
└── lfp_aggregates/
    ├── lf_compressed_v04_a14_small_all.h5    small   (ε=100, α=14)   ~11 GB
    ├── lf_compressed_v04_a07_default_all.h5  default (ε=100, α=7)    ~21.5 GB
    └── lf_compressed_v04_a2p5_fine_all.h5    fine    (ε=100, α=2.5)  ~46 GB

Each archive is a single multi-recording HDF5 file with one top-level group per insertion (pid), produced by lfpack.merge_h5.

Downloading

from pathlib import Path
from one.api import ONE
import ephysatlas.data

one = ONE(base_url='https://alyx.internationalbrainlab.org')
local_path = Path('/datadisk/ephys-atlas')
project = 'ibl_neuropixel_brainwide_01'

# default tier (~21.5 GB)
ephysatlas.data.download_lfp_features(local_path, project=project, one=one)

# small tier (~11 GB)
ephysatlas.data.download_lfp_features(
    local_path, project=project, one=one, level='small'
)

Loading

from pathlib import Path
import ephysatlas.data

local_path = Path('/datadisk/ephys-atlas')
project = 'ibl_neuropixel_brainwide_01'
pid = '00a824c0-e060-495f-9ebc-79c82fef4c67'

sr = ephysatlas.data.read_lfp_features(local_path.joinpath(project), pid)  # level='default'
traces = sr[0:2500, :]          # (2500, nc) float32, volts
sr.nc, sr.fs                    # channel count, sample rate (Hz)

read_lfp_features returns an lfpack.LFPackReader, a drop-in replacement for spikeglx.Reader — chunks are decompressed on demand. Pass bin_channels= to sum adjacent channels on read, or scale= to open a coarser pyramidal level.