Working with IBL data

Many projects make use of the large dataset collected by the International Brain Laboratory.

General info

• eLife paper describing the experiments and the behavioral data.
• Video description of the data by Eric deWitt, for NeuroMatchAcademy.
• Explore the data through the interactive data explorer.

ToDo: Colab for IBL data analysis without local Python install

See here

Behavioral data

Working with IBL behavioral data

Neural data

• See docs.internationalbrainlab.org/ for a landing page and overview.
• You can find some example data and check out analyses here.
• Browse the data in this interactive visualization app.
• See here for a tutorial given at COSYNE 2024 (recording here).
• See here for a online course on Neuropixels (recording here).

  Accessing data on ALICE

  Email the ALICE helpdesk to get access to the shared data folder: data_pi-uraiae.

Then,

# ===================================
# code to load shared (internal) data
# ===================================

import os
import pandas as pd
from one.api import ONE

# change my username to your own
project = 'churchland_learninglifespan'
save_dir = os.path.join(os.path.expanduser('~'), 'data_pi-uraiae/ONE/alyx.internationalbrainlab.org/', project)

# THIS IS THE OFFICIAL WAY - FIND THE RELEVANT SESSIONS FROM THE LOCAL CACHE
# If you want to use this cache without re-downloading data (i.e. keep the download cache the same as the main IBL Alyx), you can use the tags system.
one = ONE(mode='local', cache_dir = save_dir)
one.load_cache()
# one = ONE(mode='local')
# one.load_cache(cache_dir=save_dir)
print('Datasets location: %s;\nCache table location: %s' % (one.cache_dir, save_dir))
eids = one.search(lab='churchlandlab', query_type='local', dataset='spikes.times')
print(len(eids)) # should be 51...

# THIS IS THE HACK WAY - READ IN THOSE EIDS THAT CERTAINLY ARE AVAILABLE LOCALLY
eids = pd.read_csv(os.path.join(save_dir,'eids_on_alice.csv'))
eids = eids.eid.values
print(len(eids)) # should be 51...