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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.
Ahcore is not intended for clinical use. It is licensed under the Apache License 2.0 <https://www.apache.org/licenses/LICENSE-2.0>
_.
Ahcore comes with several models included, check the model zoo <https://docs.aiforoncology.nl/ahcore/model_zoo.html>
_ for more information:
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.