Welcome to fusilib!

What is fusilib?

fusilib is a Python package for the analysis of functional ultrasound and electrophysiology data.

Installation

The following package must be installed on your system:

• git
• pip
• python3-venv

To install the fusilib package in a virtual environment, execute the following from the command line:

git clone https://github.com/anwarnunez/fusi.git
cd fusi
python3 -m venv fusienv
source fusienv/bin/activate
pip install -r requirements.txt
pip install -e .

If you get errors from pip, try re-running the pip install commands.

Getting started

First, make sure everything is installed correctly by importing the package from within Python or IPython:

>>> import fusilib

Checkout the figshare project and download the dataset.zip file (~15GB). Unzip the file in your local machine. Then, open the command line and navigate to the unzipped Subjects folder. You should then be able to execute the demo scripts from the command line

unzip dataset.zip
cd Subjects
python3 /path/to/repo/fusi/scripts/demo.py

Alternatively, you can add the location of the downloaded data to the demo scripts directly. To do so, change the following lines at the top of the demo scripts:

# Enter the path to the downloaded "Subjects" directory.
# By default, the path is set to the current working directory.
import fusilib.config
data_location = '/path/to/extracted/data/Subjects'
fusilib.config.set_dataset_path(data_location)

Then, execute the demo script from the command line:

python3 scripts/demo.py

Cite as

Neural correlates of blood flow measured by ultrasound. Nunez-Elizalde AO, Krumin M, Reddy CB, Montaldo G, Urban A, Harris KD, and Carandini M. Neuron (2022). https://doi.org/10.1016/j.neuron.2022.02.012.