dev_brain

Developing Brain

The repository contains in vivo single unit activity (SUA) and local field potential (LFP) data recorded from several brain areas of developing mice (4-12 postnatal days):

• 3 PFC subdivisions: cingulate, prelimbic cortex and infralimbic cortex (1 Neuropixels probe, cg_pl_il_neuropixels),
• PFC (cingulate), dorsal striatum and medio-dorsal thalamus (3 Neuronexus probes, cg_str_th),
• PFC (orbitofrontal cortex), V1 and S1 (3 Neuronexus probes, v1_s1_ofc).
• PFC (PL) and HP (CA1) (2 Neuronexus probes, hp_pfc).

Data format

SUA

SUA data is provided in .csv files, one file per brain area.

Each row corresponds to one single unit and has the following format:

animal_id, age, unit_id, channel_id, spike_timepoints

important: spike timepoints are given in raw signal sampling frequency which is different for Neuropixels and Neuronexus recodings: Neuropixels 30kHz, Neuronexus 32kHz.

Every data folder includes a .xlsx file with the meta information:

• animal_id,
• sex,
• age (postnatal days),
• weight (g),
• sua_[brain_area] - for every brain area indicates whether SUA data is present in .csv files.
• sua_fs_hz - raw data sampling frequency.

LFP

LFP data is provided in .mat (cg_str_th, v1_s1_ofc) or .npy (cg_pl_il_neuropixels) format, one file per mouse per area, each file contains 2d array n_channels x n_timepoints.

In cg_str_th and v1_s1_ofc datasets raw data is preprocessed in the following way:

• band-pass filtered in the 0.1–500 Hz band (third- order Butterworth filter in a phase preserving manner)
• downsampled to 1000 Hz

In cg_pl_il_neuropixels dataset raw data is preprocessed in the following way:

• downsampled to 500 Hz

important: In cg_str_th and v1_s1_ofc datasets the first 100 seconds are cut!

Every data folder includes a .xlsx file with the meta information:

• animal_id,
• sex,
• age (postnatal days),
• weight (g),
• lfp_[brain_area] - for every brain area indicates whether LFP data data is present in the repository,
• noise_ch_l - channels that were labelled as noisy by the experimenter,
• off_target_ch_l - channels that were labelled as off target by the experimenter (column is optional),
• raw_fs_hz - raw data sampling frequency.

USV (ultrasonic vocalization), only cg_str_th

USV data is aligned with ephys data and is provided in .csv files, one file per dataset per recording type (e.g. baseline activity).

Each row corresponds to one USV call and has the following format:

animal_id, age, call_id, call_type, call_score, ephys_start_sec, ephys_end_sec, ephys_call_length

Combination of animal_id and call_id is a unique identifier.

Electrodes geometry and positions in the brain

CG-PL-IL

• One probe with 1 shank, the channels in specific area are given in .xlsx file in cg_pl_il_neuropixels folder: [brain_area]_start_ch and [brain_area]_end_ch.

OFC-V1-S1

• OFC: 16 channels probe, 4 shanks with 4 channels each.
• V1: 16 channels probe, 1 shank.
• S1: 16 channels probe, 1 shank.

CG-STR-TH

• CG: 16 channels probe, 4 shanks with 4 channels each.
• STR: 16 channels probe, 1 shank.
• TH: 16 channels probe, 1 shank.

PFC-HP

• PFC: 16 channels probe, 4 shanks with 4 channels each.
• HP: 16 channels probe, 1 shank. Units from 7 channels are included:

1. channel 4 corresponds to the "reversal" (the stratum pyramidale)
2. channels 1:3 correspond to channels that are dorsal (more superficial) to stratum pyramidale
3. channels 5:7 correspond to channels that are ventral (deeper) to stratum pyramidale