AI for Oncology Core for Computational Pathology (ahcore)

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Ahcore are the AI for Oncology <https://aiforoncology.nl>_ core components for computational pathology. It provides a set of tools for working with pathology images and annotations. It also offers standard computational pathology algorithms.

Check the full documentation <https://docs.aiforoncology.nl/ahcore>_ for more details on how to use ahcore.

License and Usage

Ahcore is not intended for clinical use. It is licensed under the Apache License 2.0 <https://www.apache.org/licenses/LICENSE-2.0>_.

Included Models

Ahcore comes with several models included, check the model zoo <https://docs.aiforoncology.nl/ahcore/model_zoo.html>_ for more information:

• Tissue/background segmentation in H&Es

Quickstart

To train a model, first make sure ahcore is installed:

git clone https://github.com/NKI-AI/ahcore.git && cd ahcore && pip install -e .

Next, make sure that the environmental variables are set correctly. We are using dotenv for this but you can set the variables themselves. Check tools/.env.example to see which variables you need to set. If you use dotenv, you will need to make a copy cp tools/.env.example tools/.env and fill in the correct values.

Next, you will need to create manifest, and once done, it's often beneficial to copy the data to a local drive, if its not there yet. You can use the ahcore data copy-data-from-manifest tool for this.