Histocartography python package. It installs histocartography
using pip
.
- OpenSlide >= 3.4.1 Source. Version 3.4.0 DOESN'T READ TIFFs properly.
- OpenCV >= 2.4
Create a virtualenv
:
python3 -m venv venv
Activate it:
source venv/bin/activate
Install the package as editable and any dependencies:
pip3 install -e .
Add these environment variables to have access to the Object Storage
export AWS_ACCESS_KEY_ID=" "
export AWS_SECRET_ACCESS_KEY=" "
There is a sample executable script in the bin/
folder that can be used
for training Histocartography machine learning pipelines.
Unit tests should be created in the test/
folder.
Run the tests with:
python3 -m unittest discover -v
The repo contains a Dockerfile
that builds an image containing the python package.