histocartography

Histocartography python package. It installs histocartography using pip.

Required libraries:

• OpenSlide >= 3.4.1 Source. Version 3.4.0 DOESN'T READ TIFFs properly.
• OpenCV >= 2.4

Suggested setup for development

Create a virtualenv:

python3 -m venv venv

Activate it:

source venv/bin/activate

Install the package as editable and any dependencies:

pip3 install -e .

Testing and Continuous Integration

Add these environment variables to have access to the Object Storage

export AWS_ACCESS_KEY_ID=" "
export AWS_SECRET_ACCESS_KEY=" "

Training

There is a sample executable script in the bin/ folder that can be used for training Histocartography machine learning pipelines.

Unit Tests

Unit tests should be created in the test/ folder. Run the tests with:

python3 -m unittest discover -v

Docker support

The repo contains a Dockerfile that builds an image containing the python package.