README.md

paper-brain-wide-map

Code related to the brainwide map paper

Installation

Create a new python environment (optional)

Install Anaconda and git, and follow their installer instructions to add each to the system path

Create new python environment

conda create --name ibl_bwm python=3.9

Activate environment

conda activate ibl_bwm

Download and Install repository

Clone the repo

git clone https://github.com/int-brain-lab/paper-brain-wide-map.git

Navigate to repo

cd paper-brain-wide-map

Install requirements and repo

pip install -e .

Install ibllib without dependencies

pip install ibllib --no-deps

To install additional requirements for the individual analyses, see the README files in the respective subfolders in brainwidemap

Query information about BWM data

You can now use the following in Python (note that ONE needs to be set up)

from brainwidemap import bwm_query, bwm_units
from one.api import ONE

one = ONE()
# Dataframe with info on all sessions and probes released for the BWM
bwm_df = bwm_query(one)
# Dataframe with information on all neurons used in the analyses in the BWM paper
unit_df = bwm_units(one)

For further data loading examples see data_loading_examples.py