1 - Download Anaconda, a free installer that includes Python and all the common scientific packages.

2- Clone (or download) the repository

(On Window, you may need to install Git)

git clone https://github.com/bioimage-analysis/Chloe_Chromosome_detection

3- Go into the directory

cd Chloe_Chromosome_detection/

4- Create a conda environment with an Ipython kernel:

(To install python / conda on a Window environment you can follow this LINK)

 conda create --name name_env python=3 ipykernel

5- Activate your conda environment:

source activate name_env

6- Install dependency from the requirements.txt :

pip install -r requirements.txt

(The installation of python-bioformats / javabridge might fail, if so, download Java Dev. kit, here)

cd to the notebook directory and lunch jupyter notebook:

jupyter notebook

You will find a basic introduction on how to use the Jupyter Notebook HERE

If it doesn't load try using this link.

Cedric Espenel
E-mail: espenel@stanford.edu