Set up

Installation

To use PENGUIN, first clone the GitHUb repo.

To clone this repository to your local machine, use the following command:

git clone https://github.com/your_username/PENGUIN.git

Environment set up

You can create the environment installing the packages or using the ymal file.

To manually create and install packages use:

conda create --name penguin
conda activate penguin
conda install matplotlib pandas panel numpy opencv scikit-image ipywidgets jupyter ipykernel plotly
pip install apeer-ometiff-library --no-deps

Alternatively, you can create the environemtn using the yml file:

conda env create --file penguin_env.yml
conda activate penguin
pip install apeer-ometiff-library --no-deps

After you created the environment, and if you want to use the Jupyter notebooks

add the environment kernel to jupyter

python -m ipykernel install --user --name=penguin

launch the jupyter and be sure that you are running with the penguin kernel.