Big-FISH examples

Big-FISH-examples is a repository where we provide images, Jupyter notebooks and Python scripts to illustrate how to use the different workflows available in Big-FISH.

smFISH image and its coordinates representation

Local installation

To avoid dependency conflicts, we recommend the the use of a dedicated virtual or conda environment. In a terminal run the command:

conda create -n bigfish_env python=X.Y

With X.Y a valid Python version greater or equal than 3.6. Note that Big-FISH is tested only for Python 3.6, 3.7, 3.8 and 3.9.

To run these notebooks, you will need to clone this repository:

git clone git@github.com:fish-quant/big-fish-examples.git

Activate your environment and install Big-FISH and Jupyter notebook dependencies inside:

source activate bigfish_env
cd big-fish-examples
pip install .

Then launch the notebooks:

jupyter notebook

Binder

You can run this examples on mybinder.org without the need for a local Python installation