Installation of PyHIST can be performed in three different ways:
- Through a Docker image (Linux/macOS/Windows)
- Conda environment (Linux/macOS)
- Standalone (Linux/macOS)
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