Local Install and Tutorial

Python

For the main required Python packages (numpy, scipy, etc.) we recommend using Anaconda for Python 3.8

Installing package and dependencies for NOVAS3D locally

  1. Clone repository

     git clone https://github.com/mrozak4/novas3d.git novas3d

 (or install zip file and uncompress)

 cd novas3d

    If you want to create a virtual environment with anaconda where NOVAS3D can be run,

     conda create -n novas3d python=3.8
 source activate novas3d

    To end the session, deactivate the environment

     source deactivate

    To delete the environment,

     conda env remove --name novas3d

    Alternative: Use virtualenv to make a virtual enviornment

     virtualenv -p python3.8 ENV
 source ENV/bin/activate

  2. Install dependencies

     pip install novas3d
 pip install git+https://github.com/Image-Py/sknw.git@18f18ab94794964a6dd7a76dd8a2c5c00dab6fd1

  3. Download example data

    Ensure git-lfs is installed and enabled or else pickle files present in the example data and model files will not download properly.

     git clone https://huggingface.co/datasets/mrozak/novas3d_example_data

  4. Download the model

     git clone https://huggingface.co/mrozak/NOVAS3D_Vessel_and_Neuron_Segmentation

  5. Test the installation by running the tutorial in jupyter

     jupyter notebook Tutorial.ipynb

Updating NOVAS3D

To update NOVAS3D, navigate to the directory where NOVAS3D was cloned and run

git pull
pip install novas3d

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