peyrache-lab-to-nwb

NWB conversion scripts for the Peyrache Lab (McGill University) data, using NeuroConv.

Related publication: Skromne Carrasco, S., Viejo, G. & Peyrache, A. Months-long stability of the head-direction system. doi: 10.1038/s41586-025-10096-w

Processed dataset: DANDI:001676

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Conversions

miniscope_arc

Converts raw UCLA Miniscope V4 calcium imaging and OptiTrack 3-D motion capture data from the SFARI ARC longitudinal head-direction study.

Data streams:

Stream	Interface	NWB output
Miniscope raw video (MJPEG .avi)	MiniscopeImagingInterface	OnePhotonSeries in acquisition
OptiTrack tracking (CSV)	OptiTrackInterface (custom)	Position + body_rotation_euler_yxz in behavior
Intan sync channels (ADC)	IntanConverter	TimeSeriesIntanSync in acquisition
Miniscope frame gate (ADC-01)	IntanConverter (analog events)	MiniscopeFrameGate events table; provides hardware timestamps

Synchronisation: Intan RHD analog inputs carry two TTL signals that hardware-stamp every Miniscope frame and every OptiTrack frame. MiniscopeArcNWBConverter.temporally_align_data_interfaces() reads the frame-gate transitions detected by NeuroConv's IntanConverter and replaces the Miniscope USB timestamps (which drift up to 236 ms over a 20-minute session) with precise hardware timestamps.

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Installation

git clone https://github.com/catalystneuro/peyrache-lab-to-nwb.git
cd peyrache-lab-to-nwb

uv venv
source .venv/bin/activate
uv pip install -e .

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Usage

Single session — new NWB file

from peyrache_lab_to_nwb.miniscope_arc.convert_session import session_to_nwb
from pathlib import Path

session_to_nwb(
    session_dir_path=Path("~/source_data/peyrache-lab/A0662/2022_07_28"),
    output_dir_path=Path("~/nwb_output/peyrache"),
    stub_test=True,  # set False for full conversion
    verbose=True,
)

Append raw Miniscope video to an existing DANDI:001676 file

# 1. Download the existing file from DANDI (requires dandi CLI)
#    dandi download "https://api.dandiarchive.org/api/assets/<asset-id>/download/"

# 2. Append raw video
session_to_nwb(
    session_dir_path=Path("~/source_data/peyrache-lab/A0662/2022_07_28"),
    output_dir_path=Path("~/nwb_output"),   # ignored in append mode
    append_to_nwb_path=Path("~/downloads/sub-A0662_ses-20220728.nwb"),
    verbose=True,
)

# 3. Re-upload with dandi CLI
#    dandi upload ~/downloads/sub-A0662_ses-20220728.nwb --dandiset 001676

All sessions

from peyrache_lab_to_nwb.miniscope_arc.convert_all_sessions import dataset_to_nwb

dataset_to_nwb(
    data_dir_path=Path("~/source_data/peyrache-lab"),
    output_dir_path=Path("~/nwb_output/peyrache"),
    max_workers=4,
    stub_test=False,
)

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Data source

Raw data are on Google Drive. Mount with rclone:

~/.local/bin/rclone nfsmount "gdrive:" "$HOME/source_data/peyrache-lab" \
  --drive-root-folder-id="1PEYVAdDfKJ4QaOsY7ivQCGnPNKsSTNTs" \
  --read-only --vfs-cache-mode full --daemon