The toolkit has been tested on Ubuntu 20.04, Ubuntu 18.04, Centos 7, cluster based on Centos 7, and MacOX. It is expected to work on Windows too. Python 3 is needed for running the toolkit. Please follow the following instructions to install and use software:

1. Install Conda from the following link: https://docs.conda.io/projects/conda/en/latest/user-guide/install/

2. Set up a virtual environment:

   conda create --name DeepLIBRA python=3.6
   

3. Activate the environment for the first time and anytime you need to work with the toolkit:

   conda activate DeepLIBRA
   

4. Install the required packages:

   pip install -r requirements.txt
   

5. The toolkit can be run either from the command line or using a graphical used interface:

   • Run toolkit using command line (there more options for running the toolkit, you can see them using -h):

     python3 Path_to_code/execute_libra_code.py -i ${Path_to_Images} -o ${Path_to_Output} -m ${Path_to_Networks}
     

     Example:

     python3 ~/Documents/MyPapers/A_Breast_Deep_LIBRA/ShortVersion/Code/execute_libra_code.py -i ~/Desktop/image -o ~/Desktop/image/output -m ~/Desktop/Nets
     

   • Run toolkit using graphical user interface:

     python3 ${Path_to_code}/run_GUI.py
     

The pretrained networks can be found from this link: https://upenn.box.com/s/y08cpr0soxxu05x5godw7h5czpn7oak8