Interactive medical image viewer for jupyter notebooks.
We recommend using Anaconda to manage dependencies and virtual environments.
- Holoviews:
conda install -c pyviz holoviews bokeh datashader panel
- xArray:
conda install -c conda-forge xarray dask netCDF4 bottleneck
- SimpleITK:
conda install -c https://conda.anaconda.org/simpleitk SimpleITK
git clone https://github.com/pollackscience/pyviz_med
cd pyviz_med
pip install -e .
cd ..
- Download the CHAOS abdominal segmentation data (https://zenodo.org/record/3431873):
cd pyviz_med/data/CHAOS
wget -O CHAOS.zip https://zenodo.org/record/3431873/files/CHAOS_Train_Sets.zip?download=1
unzip CHAOS.zip
- Open up the jupyter notebook
pyviz_med/notebook/CHAOS_Tutorial.ipynb
- Run all cells!
Brian Pollack 2020 University of Pittsburgh