Installation of PyHIST can be performed in three different ways:

PyHIST Docker image (Linux/macOS/Windows)

The Docker image described in this section contains all the necessary dependencies to run PyHIST. The public Docker image for PyHIST can be downloaded from the Docker Hub:

docker pull mmunozag/pyhist

After downloading it, you can skip directly to Quickstart: Using the Docker image. Alternatively, you can build the Docker image on your own by using the Dockerfile in this repository. Clone the respository and move into the folder:

git clone https://github.com/manuel-munoz-aguirre/PyHIST.git
cd PyHIST

Build the docker image with the following command:

docker build -f docker/Dockerfile -t mmunozag/pyhist .

Conda environment (Linux/macOS)

Clone the respository and move into the folder:

git clone https://github.com/manuel-munoz-aguirre/PyHIST.git
cd PyHIST

A conda environment with all the necessary Python dependencies can be created with:

conda env create -f conda/environment.yml

Then, PyHIST can be simply used as a python script (see quickstart).

Standalone installation (Linux/macOS)

Although we recommend isolating all the dependencies in a conda environment as above, PyHIST can be simply used as a python script (see quickstart) as long as the following dependencies are met:

  • Python (>3.6):
  • openslide-python, opencv-python, pandas, numpy, Pillow
  • Other:
  • openslide-tools, pixman==0.36.0