The jupyter notebook workflow_example.ipynb shows the workflow and it's output using example data. In this notebook, the steps are identified for better understanding.
Data used in the workflow_example.ipynb is located in the example_data/ folder.
The bacterial_identification was developped in python3 and can be easily installed through the python wheel. The repo must be cloned first and then the package can be installed using the following commands lines in the desired folder :
git clone https://github.com/Hanene-Mansour/bacterialidentification.git
pip install path/to/bacterial_identification/
Hardware:
- A CUDA capable GPU is recommended.
- At least 3 GB of storage.
- Python 3.8.5
- matplotlib 3.3.0
- numpy 1.19.1
- scipy 0.10.1