PyViz Med

Interactive medical image viewer for jupyter notebooks.

Installation

We recommend using Anaconda to manage dependencies and virtual environments.

Dependencies:

1. Holoviews: conda install -c pyviz holoviews bokeh datashader panel
2. xArray: conda install -c conda-forge xarray dask netCDF4 bottleneck
3. SimpleITK: conda install -c https://conda.anaconda.org/simpleitk SimpleITK

Pyviz_med

git clone https://github.com/pollackscience/pyviz_med
cd pyviz_med
pip install -e .
cd ..

Basic Tutorial

1. 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
2. Open up the jupyter notebook pyviz_med/notebook/CHAOS_Tutorial.ipynb
3. Run all cells!

Brian Pollack 2020 University of Pittsburgh