Docker container for BaSiCPy

https://hub.docker.com/r/yfukai/basicpy-docker-mcmicro

About this repository

This is a simple Docker container wrapping BaSiCPy, intended to be used in MCMICRO.

Please run this container as

# with CPU
docker run --rm -v /path/to/data:/data ghcr.io/yfukai/basicpy-docker-mcmicro:latest --cpu /data/filename.ome.tiff -o /data/
# with CUDA >= 11.5
docker run --rm -v /path/to/data:/data ghcr.io/yfukai/basicpy-docker-mcmicro:latest-cuda --gpu /data/filename.ome.tiff -o /data/

and you'll find the files filename-ffp.tiff (for the flatfield) and filename-dfp.tiff (for the darkfield).

For development

Please install pre-commit as follows.

pip install pre-commit
pre-commit install