Moving the configurations in a configuration file

BodenmillerGroup / ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline

https://bodenmillergroup.github.io/ImcSegmentationPipeline/

MIT License

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Moving the configurations in a configuration file #6

Closed votti closed 2 years ago

votti commented 5 years ago

Currently, the configurations for the pipeline are handled at the beginning of a jupyter notebook. In the spirit of also allowing the pipeline to be reproducibly run from the command line, using a configuration file would be more appropriate.

nilseling commented 2 years ago

Command line calls are now supported by steinbock