MONAI
Medical Open Network for AI
New milestone release changes: https://docs.monai.io/en/latest/whatsnew.html
Transfer learning from Clara Train models: https://github.com/Project-MONAI/tutorials/blob/master/modules/transfer_mmar.ipynb
Requires PyTorch
Would be considered sofware of unknown provenance
MONAI Installation
Installation guide: https://docs.monai.io/en/latest/installation.html
Install current milestone release:
pip install monai
Note
Alternatively, you can install the weekly release for the latest features:
pip install monai-weekly
Validate installation by running this, which should return the installed MONAI version information:
python -c 'import monai; monai.config.print_config()'
Install all optional dependencies:
pip install 'monai[all]'
MONAI Label
“For Researchers, MONAI Label gives you an easy way to define their pipeline to facilitate the image annotation process.For Clinicians, MONAI Label gives you access to a continuously learning AI that will better understand what the end-user is trying to annotate. MONAI Label comprises the following key components: MONAI Label Server, MONAI Label Sample Apps, MONAI Label Sample Datasets, and a 3DSlicer Viewer extension.”
“Create MONAI Label Apps using the three different paradigms: DeepGrow, DeepEdit, and automatic segmentation.”
Claims it supports Ubuntu and Windows with GPU/CUDA enabled.
MONAI Label Installation
Official installation guide: https://docs.monai.io/projects/label/en/latest/installation.html
Install Python libraries:
pip install testresources
python -m pip install --upgrade pip setuptools wheel
Install current milestone release:
pip install monailabel
Note
Alternatively, you can install the weekly release for the latest features:
pip install monailabel-weekly
Install from GitHub
You can alternatively install the latest version from the GitHub main branch, although it takes longer.
Install git:
sudo apt install git
Install the latest version from the GitHub main branch:
pip install git+https://github.com/Project-MONAI/MONAILabel#egg=monailabel
Tip
If you want to update to the weekly or GitHub version, uninstall monailabel first:
sudo pip uninstall monailabel
If that didn’t uninstall it, remove sudo:
pip uninstall monailabel
Run monailabel --help to see if Monai Label installed correctly. If it says “python: command not found,” you may have a monailabel file in ~/.local/bin/ that you need to edit. Comment everything out (put a # at the beginning of a line) until this is the only executed code:
set -e
PYEXE=python3
${PYEXE} -m monailabel.main $*
Update MONAI
To update an install of MONAI to a new stable version, you need to first uninstall MONAI and MONAI Label:
pip uninstall monailabel
pip uninstall monai
Then, install MONAI, optional dependencies, and MONAI Label:
pip install monai
pip install 'monai[all]'
pip install monailabel